Genetic Variant SLC9B2:c.-42-150C>A (chr4-103067742-G-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_178833.7(SLC9B2):c.-42-150C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.454 in 552,728 control chromosomes in the GnomAD database, including 61,818 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 0.54 ( 24390 hom., cov: 32)

Exomes 𝑓: 0.42 ( 37428 hom. )

Consequence

SLC9B2
NM_178833.7 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.691

Publications

24 publications found

Variant links:

Genes affected

SLC9B2 (HGNC:25143): (solute carrier family 9 member B2) Sodium hydrogen antiporters, such as NHEDC2, convert the proton motive force established by the respiratory chain or the F1F0 mitochondrial ATPase into sodium gradients that drive other energy-requiring processes, transduce environmental signals into cell responses, or function in drug efflux (Xiang et al., 2007 [PubMed 18000046]).[supplied by OMIM, Mar 2008]

SLC9B2 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=-0.92).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.828 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_178833.7. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
SLC9B2	NM_178833.7	MANE Select	c.-42-150C>A	intron	N/A	NP_849155.2
SLC9B2	NM_001370201.1		c.-42-150C>A	intron	N/A	NP_001357130.1	Q86UD5-1
SLC9B2	NM_001370202.1		c.-42-150C>A	intron	N/A	NP_001357131.1	Q86UD5-1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
SLC9B2	ENST00000394785.9	TSL:2 MANE Select	c.-42-150C>A	intron	N/A	ENSP00000378265.3	Q86UD5-1
SLC9B2	ENST00000362026.7	TSL:1	c.-42-150C>A	intron	N/A	ENSP00000354574.3	Q86UD5-1
SLC9B2	ENST00000890707.1		c.-42-150C>A	intron	N/A	ENSP00000560766.1

Frequencies

GnomAD3 genomes

AF:

0.536

AC:

81340

AN:

151862

Hom.:

24327

Cov.:

show subpopulations

Gnomad AFR

AF:

0.835

Gnomad AMI

AF:

0.350

Gnomad AMR

AF:

0.462

Gnomad ASJ

AF:

0.426

Gnomad EAS

AF:

0.395

Gnomad SAS

AF:

0.419

Gnomad FIN

AF:

0.431

Gnomad MID

AF:

0.541

Gnomad NFE

AF:

0.414

Gnomad OTH

AF:

0.506

GnomAD4 exome

AF:

0.423

AC:

169647

AN:

400748

Hom.:

37428

AF XY:

0.421

AC XY:

89934

AN XY:

213626

show subpopulations

African (AFR)

AF:

0.833

AC:

9226

AN:

11076

American (AMR)

AF:

0.459

AC:

7488

AN:

16306

Ashkenazi Jewish (ASJ)

AF:

0.413

AC:

5066

AN:

12266

East Asian (EAS)

AF:

0.365

AC:

10006

AN:

27396

South Asian (SAS)

AF:

0.404

AC:

16473

AN:

40806

European-Finnish (FIN)

AF:

0.411

AC:

10114

AN:

24632

Middle Eastern (MID)

AF:

0.515

AC:

884

AN:

1718

European-Non Finnish (NFE)

AF:

0.411

AC:

100034

AN:

243620

Other (OTH)

AF:

0.452

AC:

10356

AN:

22928

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.492

Heterozygous variant carriers

4296

8592

12888

17184

21480

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

568

1136

1704

2272

2840

<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:

0.536

AC:

81465

AN:

151980

Hom.:

24390

Cov.:

AF XY:

0.532

AC XY:

39516

AN XY:

74310

show subpopulations

African (AFR)

AF:

0.836

AC:

34686

AN:

41502

American (AMR)

AF:

0.463

AC:

7061

AN:

15266

Ashkenazi Jewish (ASJ)

AF:

0.426

AC:

1474

AN:

3462

East Asian (EAS)

AF:

0.397

AC:

2049

AN:

5164

South Asian (SAS)

AF:

0.419

AC:

2021

AN:

4824

European-Finnish (FIN)

AF:

0.431

AC:

4539

AN:

10530

Middle Eastern (MID)

AF:

0.531

AC:

156

AN:

294

European-Non Finnish (NFE)

AF:

0.414

AC:

28101

AN:

67916

Other (OTH)

AF:

0.502

AC:

1059

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1681

3362

5044

6725

8406

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

674

1348

2022

2696

3370

<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:

0.426

Hom.:

10442

Bravo

AF:

0.554

Asia WGS

AF:

0.440

AC:

1527

AN:

3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

0.11

(source)

DANN

Benign

0.20

PhyloP100

-0.69

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over