4-103067742-G-T

Variant names:

• chr4-103067742-G-T
• rs7674212
• NM_178833.7:c.-42-150C>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.691
• Publications: 24 publications found

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]

ACMG classification

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC9B2	NM_178833.7	c.-42-150C>A		intron_variant	Intron 1 of 11	ENST00000394785.9	NP_849155.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC9B2	ENST00000394785.9	c.-42-150C>A		intron_variant	Intron 1 of 11	2	NM_178833.7	ENSP00000378265.3

Frequencies

GnomAD3 genomes AF: 0.536 AC: 81340 AN: 151862 Hom.: 24327 Cov.: 32

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

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

GnomAD4 genome AF: 0.536 AC: 81465 AN: 151980 Hom.: 24390 Cov.: 32 AF XY: 0.532 AC XY: 39516 AN XY: 74310

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

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.11
DANN	Benign	0.20
PhyloP100		-0.69
Mutation Taster		=100/0	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

Other links and lift over

dbSNP: rs7674212; hg19: chr4-103988899;