dbSNP rs17136953: UMAD1:c.82+62431A>G (chr7-7735884-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001302348.2(UMAD1):c.82+62431A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.297 in 152,210 control chromosomes in the GnomAD database, including 7,761 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.30 ( 7759 hom., cov: 32)

Exomes 𝑓: 0.39 ( 2 hom. )

Consequence

UMAD1
NM_001302348.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.443

Publications

3 publications found

Variant links:

Genes affected

UMAD1 (HGNC:48955): (UBAP1-MVB12-associated (UMA) domain containing 1)

UMAD1 links:

ENSG00000270314 (HGNC:):

ENSG00000270314 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.91).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.477 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
UMAD1	NM_001302348.2 link	c.82+62431A>G	intron_variant	Intron 2 of 3	ENST00000682710.1	NP_001289277.1	C9J7I0
LOC100533631		n.7735884A>G	intragenic_variant
UMAD1	NM_001302349.2 link	c.82+62431A>G	intron_variant	Intron 2 of 3		NP_001289278.1	C9J7I0
UMAD1	NM_001302350.2 link	c.-24+59676A>G	intron_variant	Intron 3 of 4		NP_001289279.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
UMAD1	ENST00000682710.1 link	c.82+62431A>G		intron_variant	Intron 2 of 3		NM_001302348.2	ENSP00000507605.1		C9J7I0

Frequencies

GnomAD3 genomes

AF:

0.297

AC:

45163

AN:

152074

Hom.:

7741

Cov.:

show subpopulations

Gnomad AFR

AF:

0.482

Gnomad AMI

AF:

0.446

Gnomad AMR

AF:

0.208

Gnomad ASJ

AF:

0.236

Gnomad EAS

AF:

0.221

Gnomad SAS

AF:

0.274

Gnomad FIN

AF:

0.199

Gnomad MID

AF:

0.323

Gnomad NFE

AF:

0.228

Gnomad OTH

AF:

0.290

GnomAD4 exome

AF:

0.389

AC:

AN:

Hom.:

Cov.:

AF XY:

0.500

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.125

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.600

AC:

AN:

Other (OTH)

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.575

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<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:

0.297

AC:

45221

AN:

152192

Hom.:

7759

Cov.:

AF XY:

0.293

AC XY:

21775

AN XY:

74414

show subpopulations

African (AFR)

AF:

0.482

AC:

20019

AN:

41496

American (AMR)

AF:

0.208

AC:

3173

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.236

AC:

818

AN:

3470

East Asian (EAS)

AF:

0.222

AC:

1152

AN:

5194

South Asian (SAS)

AF:

0.273

AC:

1320

AN:

4832

European-Finnish (FIN)

AF:

0.199

AC:

2105

AN:

10576

Middle Eastern (MID)

AF:

0.333

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.228

AC:

15513

AN:

68012

Other (OTH)

AF:

0.291

AC:

616

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1549

3097

4646

6194

7743

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

440

880

1320

1760

2200

<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:

0.258

Hom.:

750

Bravo

AF:

0.307

Asia WGS

AF:

0.313

AC:

1087

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

1.7

(source)

DANN

Benign

0.60

PhyloP100

0.44

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over