dbSNP rs4151150: MNAT1:p.Ser18Ser (chr14-60734916-C-T) – ACMG Classification: Benign (-11 pts)

Variant summary

Our verdict is Benign. The variant received -11 ACMG points: 0P and 11B. BP4_ModerateBP7BA1

The NM_002431.4(MNAT1):c.54C>T(p.Ser18Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0161 in 1,614,102 control chromosomes in the GnomAD database, including 400 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 0.016 ( 40 hom., cov: 32)

Exomes 𝑓: 0.016 ( 360 hom. )

Consequence

MNAT1
NM_002431.4 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.188

Publications

9 publications found

Variant links:

Genes affected

MNAT1 (HGNC:7181): (MNAT1 component of CDK activating kinase) The protein encoded by this gene, along with cyclin H and CDK7, forms the CDK-activating kinase (CAK) enzymatic complex. This complex activates several cyclin-associated kinases and can also associate with TFIIH to activate transcription by RNA polymerase II. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2011]

MNAT1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -11 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.31).

BP7

Synonymous conserved (PhyloP=-0.188 with no splicing effect.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0538 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MNAT1	NM_002431.4 link	c.54C>T	p.Ser18Ser	synonymous_variant	Exon 1 of 8	ENST00000261245.9	NP_002422.1	P51948-1A0A024R688
MNAT1	NM_001177963.2 link	c.54C>T	p.Ser18Ser	synonymous_variant	Exon 1 of 7		NP_001171434.1	P51948-2A0A024R669
MNAT1	XM_005267688.4 link	c.54C>T	p.Ser18Ser	synonymous_variant	Exon 1 of 8		XP_005267745.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MNAT1	ENST00000261245.9 link	c.54C>T	p.Ser18Ser	synonymous_variant	Exon 1 of 8	1	NM_002431.4	ENSP00000261245.4		P51948-1

Frequencies

GnomAD3 genomes

AF:

0.0161

AC:

2443

AN:

152126

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0224

Gnomad AMI

AF:

0.0318

Gnomad AMR

AF:

0.0107

Gnomad ASJ

AF:

0.00980

Gnomad EAS

AF:

0.000385

Gnomad SAS

AF:

0.0592

Gnomad FIN

AF:

0.00688

Gnomad MID

AF:

0.0411

Gnomad NFE

AF:

0.0127

Gnomad OTH

AF:

0.0248

GnomAD2 exomes

AF:

0.0176

AC:

4436

AN:

251470

AF XY:

0.0201

show subpopulations

Gnomad AFR exome

AF:

0.0213

Gnomad AMR exome

AF:

0.00723

Gnomad ASJ exome

AF:

0.0132

Gnomad EAS exome

AF:

0.000272

Gnomad FIN exome

AF:

0.00564

Gnomad NFE exome

AF:

0.0138

Gnomad OTH exome

AF:

0.0145

GnomAD4 exome

AF:

0.0161

AC:

23503

AN:

1461858

Hom.:

360

Cov.:

AF XY:

0.0174

AC XY:

12638

AN XY:

727228

show subpopulations

African (AFR)

AF:

0.0232

AC:

776

AN:

33476

American (AMR)

AF:

0.00738

AC:

330

AN:

44724

Ashkenazi Jewish (ASJ)

AF:

0.0148

AC:

386

AN:

26134

East Asian (EAS)

AF:

0.000227

AC:

AN:

39700

South Asian (SAS)

AF:

0.0631

AC:

5446

AN:

86250

European-Finnish (FIN)

AF:

0.00584

AC:

312

AN:

53418

Middle Eastern (MID)

AF:

0.0420

AC:

242

AN:

5768

European-Non Finnish (NFE)

AF:

0.0134

AC:

14876

AN:

1111992

Other (OTH)

AF:

0.0186

AC:

1126

AN:

60396

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.463

Heterozygous variant carriers

1170

2340

3510

4680

5850

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

614

1228

1842

2456

3070

<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:

0.0161

AC:

2444

AN:

152244

Hom.:

Cov.:

AF XY:

0.0166

AC XY:

1233

AN XY:

74442

show subpopulations

African (AFR)

AF:

0.0224

AC:

931

AN:

41550

American (AMR)

AF:

0.0106

AC:

162

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.00980

AC:

AN:

3468

East Asian (EAS)

AF:

0.000386

AC:

AN:

5186

South Asian (SAS)

AF:

0.0594

AC:

286

AN:

4812

European-Finnish (FIN)

AF:

0.00688

AC:

AN:

10618

Middle Eastern (MID)

AF:

0.0442

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0127

AC:

863

AN:

68002

Other (OTH)

AF:

0.0241

AC:

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

116

232

349

465

581

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

102

136

170

<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:

0.0132

Hom.:

Bravo

AF:

0.0152

Asia WGS

AF:

0.0250

AC:

AN:

3478

EpiCase

AF:

0.0144

EpiControl

AF:

0.0158

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.31

CADD

Benign

8.2

(source)

DANN

Benign

0.91

PhyloP100

-0.19

PromoterAI

-0.018

Neutral

(source)

Mutation Taster

=100/0

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

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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