Genetic Variant SLC9A4:p.Ser121Ser (chr2-102478945-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_001011552.4(SLC9A4):c.363G>A(p.Ser121Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.45 in 1,613,808 control chromosomes in the GnomAD database, including 168,329 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as association (no stars).

Frequency

Genomes: 𝑓 0.42 ( 14130 hom., cov: 33)

Exomes 𝑓: 0.45 ( 154199 hom. )

Consequence

SLC9A4
NM_001011552.4 synonymous

Scores

Clinical Significance

association no assertion criteria provided O:1

Conservation

PhyloP100: -0.426

Variant links:

Genes affected

SLC9A4 (HGNC:11077): (solute carrier family 9 member A4) Predicted to enable potassium:proton antiporter activity and sodium:proton antiporter activity. Predicted to be involved in potassium ion transmembrane transport; regulation of intracellular pH; and sodium ion import across plasma membrane. Predicted to act upstream of or within epithelial cell development and gastric acid secretion. Predicted to be located in several cellular components, including apical plasma membrane; basolateral plasma membrane; and vacuolar membrane. Predicted to be integral component of membrane. Predicted to be active in plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

SLC9A4 links:

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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=-0.75).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.481 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC9A4	NM_001011552.4 link	c.363G>A	p.Ser121Ser	synonymous_variant	Exon 2 of 12	ENST00000295269.5	NP_001011552.2	Q6AI14
SLC9A4	XM_011511158.2 link	c.363G>A	p.Ser121Ser	synonymous_variant	Exon 2 of 12		XP_011509460.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC9A4	ENST00000295269.5 link	c.363G>A	p.Ser121Ser	synonymous_variant	Exon 2 of 12	1	NM_001011552.4	ENSP00000295269.4		Q6AI14

Frequencies

GnomAD3 genomes

AF:

0.416

AC:

63229

AN:

151910

Hom.:

14122

Cov.:

show subpopulations

Gnomad AFR

AF:

0.294

Gnomad AMI

AF:

0.502

Gnomad AMR

AF:

0.368

Gnomad ASJ

AF:

0.465

Gnomad EAS

AF:

0.226

Gnomad SAS

AF:

0.356

Gnomad FIN

AF:

0.612

Gnomad MID

AF:

0.465

Gnomad NFE

AF:

0.485

Gnomad OTH

AF:

0.444

GnomAD2 exomes

AF:

0.418

AC:

104990

AN:

251356

AF XY:

0.425

show subpopulations

Gnomad AFR exome

AF:

0.285

Gnomad AMR exome

AF:

0.292

Gnomad ASJ exome

AF:

0.458

Gnomad EAS exome

AF:

0.234

Gnomad FIN exome

AF:

0.604

Gnomad NFE exome

AF:

0.480

Gnomad OTH exome

AF:

0.447

GnomAD4 exome

AF:

0.454

AC:

662918

AN:

1461778

Hom.:

154199

Cov.:

AF XY:

0.453

AC XY:

329395

AN XY:

727202

show subpopulations

Gnomad4 AFR exome

AF:

0.295

AC:

9862

AN:

33480

Gnomad4 AMR exome

AF:

0.300

AC:

13409

AN:

44724

Gnomad4 ASJ exome

AF:

0.456

AC:

11931

AN:

26136

Gnomad4 EAS exome

AF:

0.208

AC:

8249

AN:

39682

Gnomad4 SAS exome

AF:

0.352

AC:

30351

AN:

86256

Gnomad4 FIN exome

AF:

0.597

AC:

31853

AN:

53340

Gnomad4 NFE exome

AF:

0.475

AC:

527880

AN:

1111996

Gnomad4 Remaining exome

AF:

0.441

AC:

26643

AN:

60396

Heterozygous variant carriers

24690

49380

74071

98761

123451

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Exome Het

Exome Hom

Variant carriers

15324

30648

45972

61296

76620

<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:

0.416

AC:

63256

AN:

152030

Hom.:

14130

Cov.:

AF XY:

0.420

AC XY:

31238

AN XY:

74300

show subpopulations

Gnomad4 AFR

AF:

0.293

AC:

0.293443

AN:

0.293443

Gnomad4 AMR

AF:

0.367

AC:

0.367279

AN:

0.367279

Gnomad4 ASJ

AF:

0.465

AC:

0.464553

AN:

0.464553

Gnomad4 EAS

AF:

0.227

AC:

0.226796

AN:

0.226796

Gnomad4 SAS

AF:

0.355

AC:

0.355247

AN:

0.355247

Gnomad4 FIN

AF:

0.612

AC:

0.612247

AN:

0.612247

Gnomad4 NFE

AF:

0.485

AC:

0.485185

AN:

0.485185

Gnomad4 OTH

AF:

0.447

AC:

0.446547

AN:

0.446547

Heterozygous variant carriers

1822

3644

5466

7288

9110

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Genome Het

Genome Hom

Variant carriers

592

1184

1776

2368

2960

<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:

0.449

Hom.:

49607

Bravo

AF:

0.389

Asia WGS

AF:

0.327

AC:

1140

AN:

3478

EpiCase

AF:

0.486

EpiControl

AF:

0.484

ClinVar

Significance: association

Submissions summary: Other:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

Ascending aortic dissection

Other:1

Feb 01, 2021

Beijing Anzhen Hospital, Capital Medical University

Significance:association

Review Status:no assertion criteria provided

Collection Method:case-control

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.75

CADD

Benign

2.6

DANN

Benign

0.90

Mutation Taster

=98/2

polymorphism (auto)

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over