dbSNP rs73376010: NUTM1:c.-35G>C (chr15-34343662-G-C) – ACMG Classification: Benign (-20 pts)

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001284293.2(NUTM1):c.30G>C(p.Lys10Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.149 in 1,533,972 control chromosomes in the GnomAD database, including 18,178 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/16 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.15 ( 1795 hom., cov: 32)

Exomes 𝑓: 0.15 ( 16383 hom. )

Consequence

NUTM1
NM_001284293.2 missense

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.134

Publications

7 publications found

Variant links:

Genes affected

NUTM1 (HGNC:29919): (NUT midline carcinoma family member 1) Predicted to be located in cytoplasm and nucleus. [provided by Alliance of Genome Resources, Apr 2022]

NUTM1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -20 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0044864714).

BP6

Variant 15-34343662-G-C is Benign according to our data. Variant chr15-34343662-G-C is described in ClinVar as Benign. ClinVar VariationId is 403246.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.316 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001284293.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
NUTM1	NM_001284292.2	MANE Select	c.-35G>C		5_prime_UTR	Exon 1 of 8	NP_001271221.2	Q86Y26-4
NUTM1	NM_001284293.2		c.30G>C	p.Lys10Asn	missense	Exon 1 of 7	NP_001271222.2	Q86Y26-3
NUTM1	NM_175741.3		c.-204G>C		5_prime_UTR	Exon 1 of 8	NP_786883.2	Q86Y26-1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
NUTM1	ENST00000537011.6	TSL:2 MANE Select	c.-35G>C		5_prime_UTR	Exon 1 of 8	ENSP00000444896.1	Q86Y26-4
NUTM1	ENST00000333756.5	TSL:1	c.-204G>C		5_prime_UTR	Exon 1 of 8	ENSP00000329448.4	Q86Y26-1
NUTM1	ENST00000438749.7	TSL:2	c.30G>C	p.Lys10Asn	missense	Exon 1 of 7	ENSP00000407031.3	Q86Y26-3

Frequencies

GnomAD3 genomes

AF:

0.150

AC:

22775

AN:

152102

Hom.:

1793

Cov.:

show subpopulations

Gnomad AFR

AF:

0.144

Gnomad AMI

AF:

0.235

Gnomad AMR

AF:

0.161

Gnomad ASJ

AF:

0.118

Gnomad EAS

AF:

0.329

Gnomad SAS

AF:

0.204

Gnomad FIN

AF:

0.104

Gnomad MID

AF:

0.149

Gnomad NFE

AF:

0.141

Gnomad OTH

AF:

0.148

GnomAD2 exomes

AF:

0.168

AC:

21590

AN:

128342

AF XY:

0.170

show subpopulations

Gnomad AFR exome

AF:

0.153

Gnomad AMR exome

AF:

0.158

Gnomad ASJ exome

AF:

0.125

Gnomad EAS exome

AF:

0.319

Gnomad FIN exome

AF:

0.110

Gnomad NFE exome

AF:

0.141

Gnomad OTH exome

AF:

0.165

GnomAD4 exome

AF:

0.149

AC:

206075

AN:

1381752

Hom.:

16383

Cov.:

AF XY:

0.151

AC XY:

102664

AN XY:

681866

show subpopulations

African (AFR)

AF:

0.150

AC:

4732

AN:

31544

American (AMR)

AF:

0.161

AC:

5737

AN:

35686

Ashkenazi Jewish (ASJ)

AF:

0.127

AC:

3198

AN:

25162

East Asian (EAS)

AF:

0.302

AC:

10802

AN:

35722

South Asian (SAS)

AF:

0.202

AC:

15968

AN:

79194

European-Finnish (FIN)

AF:

0.115

AC:

3854

AN:

33444

Middle Eastern (MID)

AF:

0.139

AC:

792

AN:

5688

European-Non Finnish (NFE)

AF:

0.141

AC:

152448

AN:

1077462

Other (OTH)

AF:

0.148

AC:

8544

AN:

57850

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.484

Heterozygous variant carriers

8019

16037

24056

32074

40093

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

5718

11436

17154

22872

28590

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.150

AC:

22788

AN:

152220

Hom.:

1795

Cov.:

AF XY:

0.153

AC XY:

11424

AN XY:

74434

show subpopulations

African (AFR)

AF:

0.144

AC:

5979

AN:

41536

American (AMR)

AF:

0.162

AC:

2475

AN:

15302

Ashkenazi Jewish (ASJ)

AF:

0.118

AC:

411

AN:

3472

East Asian (EAS)

AF:

0.329

AC:

1705

AN:

5176

South Asian (SAS)

AF:

0.203

AC:

978

AN:

4818

European-Finnish (FIN)

AF:

0.104

AC:

1105

AN:

10592

Middle Eastern (MID)

AF:

0.146

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.141

AC:

9566

AN:

68006

Other (OTH)

AF:

0.148

AC:

312

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1006

2013

3019

4026

5032

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

258

516

774

1032

1290

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.139

Hom.:

267

Bravo

AF:

0.154

TwinsUK

AF:

0.135

AC:

502

ALSPAC

AF:

0.148

AC:

572

ExAC

AF:

0.157

AC:

2147

Asia WGS

AF:

0.222

AC:

772

AN:

3478

ClinVar

ClinVar submissions

Significance:Benign

Revision:criteria provided, multiple submitters, no conflicts

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (1)

not specified (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.17

BayesDel_addAF

Benign

-0.77

BayesDel_noAF

Benign

-0.74

CADD

Benign

7.7

(source)

DANN

Benign

0.50

Eigen

Benign

-0.86

Eigen_PC

Benign

-0.78

FATHMM_MKL

Benign

0.16

LIST_S2

Benign

0.25

MetaRNN

Benign

0.0045

MetaSVM

Benign

-0.91

PhyloP100

-0.13

PROVEAN

Benign

0.090

REVEL

Benign

0.023

Sift

Benign

1.0

Sift4G

Benign

0.71

Vest4

0.065

MutPred

0.15

Loss of MoRF binding (P = 0.0167)

ClinPred

0.0035

GERP RS

2.1

PromoterAI

0.0012

Neutral

(source)

Mutation Taster

=300/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over