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

new If you want to explore the variant's impact on the transcript NM_002431.4, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_002431.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MNAT1	NM_002431.4	MANE Select	c.54C>T	p.Ser18Ser	synonymous	Exon 1 of 8	NP_002422.1	A0A024R688
	MNAT1	NM_001177963.2		c.54C>T	p.Ser18Ser	synonymous	Exon 1 of 7	NP_001171434.1	P51948-2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
MNAT1	ENST00000261245.9	TSL:1 MANE Select	c.54C>T	p.Ser18Ser	synonymous	Exon 1 of 8	ENSP00000261245.4	P51948-1
MNAT1	ENST00000539616.6	TSL:1	c.54C>T	p.Ser18Ser	synonymous	Exon 1 of 7	ENSP00000446437.2	P51948-2
MNAT1	ENST00000556764.5	TSL:1	n.144C>T		non_coding_transcript_exon	Exon 1 of 4

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

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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