dbSNP rs7186310: SLC9A5:n.3410A>C (chr16-67271610-A-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000563723.5(SLC9A5):n.3410A>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.226 in 205,502 control chromosomes in the GnomAD database, including 10,434 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 0.26 ( 9596 hom., cov: 32)

Exomes 𝑓: 0.12 ( 838 hom. )

Consequence

SLC9A5
ENST00000563723.5 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0730

Publications

19 publications found

Variant links:

Genes affected

SLC9A5 (HGNC:11078): (solute carrier family 9 member A5) 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 be integral component of membrane. Predicted to be active in plasma membrane. Implicated in end stage renal disease. [provided by Alliance of Genome Resources, Apr 2022]

SLC9A5 links:

LOC124903701 (HGNC:):

LOC124903701 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=-0.89).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.636 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC9A5	NM_004594.3 link	c.*400A>C		3_prime_UTR_variant	Exon 16 of 16	ENST00000299798.16	NP_004585.1	Q14940Q9NSW9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC9A5	ENST00000299798.16 link	c.*400A>C		3_prime_UTR_variant	Exon 16 of 16	1	NM_004594.3	ENSP00000299798.11		Q14940

Frequencies

GnomAD3 genomes

AF:

0.262

AC:

39807

AN:

151960

Hom.:

9555

Cov.:

show subpopulations

Gnomad AFR

AF:

0.642

Gnomad AMI

AF:

0.174

Gnomad AMR

AF:

0.150

Gnomad ASJ

AF:

0.0864

Gnomad EAS

AF:

0.0205

Gnomad SAS

AF:

0.174

Gnomad FIN

AF:

0.159

Gnomad MID

AF:

0.225

Gnomad NFE

AF:

0.108

Gnomad OTH

AF:

0.215

GnomAD4 exome

AF:

0.124

AC:

6627

AN:

53424

Hom.:

838

Cov.:

AF XY:

0.124

AC XY:

3452

AN XY:

27842

show subpopulations

African (AFR)

AF:

0.650

AC:

1319

AN:

2030

American (AMR)

AF:

0.123

AC:

491

AN:

3978

Ashkenazi Jewish (ASJ)

AF:

0.0915

AC:

121

AN:

1322

East Asian (EAS)

AF:

0.0156

AC:

AN:

3082

South Asian (SAS)

AF:

0.159

AC:

896

AN:

5640

European-Finnish (FIN)

AF:

0.132

AC:

280

AN:

2126

Middle Eastern (MID)

AF:

0.124

AC:

AN:

202

European-Non Finnish (NFE)

AF:

0.0957

AC:

3083

AN:

32218

Other (OTH)

AF:

0.129

AC:

364

AN:

2826

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.513

Heterozygous variant carriers

260

520

780

1040

1300

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

156

234

312

390

<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:

0.262

AC:

39906

AN:

152078

Hom.:

9596

Cov.:

AF XY:

0.259

AC XY:

19293

AN XY:

74364

show subpopulations

African (AFR)

AF:

0.643

AC:

26649

AN:

41468

American (AMR)

AF:

0.150

AC:

2286

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.0864

AC:

300

AN:

3472

East Asian (EAS)

AF:

0.0206

AC:

106

AN:

5152

South Asian (SAS)

AF:

0.173

AC:

835

AN:

4818

European-Finnish (FIN)

AF:

0.159

AC:

1685

AN:

10580

Middle Eastern (MID)

AF:

0.218

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.108

AC:

7370

AN:

67978

Other (OTH)

AF:

0.214

AC:

452

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.509

Heterozygous variant carriers

1114

2228

3343

4457

5571

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

344

688

1032

1376

1720

<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:

0.141

Hom.:

4580

Bravo

AF:

0.275

Asia WGS

AF:

0.155

AC:

539

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

1.7

(source)

DANN

Benign

0.43

PhyloP100

-0.073

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