4-103067742-G-T

Position:

• chr4-103067742-G-T

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
SLC9B2	NM_178833.7	c.-42-150C>A		intron_variant		ENST00000394785.9	NP_849155.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC9B2	ENST00000394785.9	c.-42-150C>A		intron_variant		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

Gnomad4 AFR exome AF: 0.833

Gnomad4 AMR exome AF: 0.459

Gnomad4 ASJ exome AF: 0.413

Gnomad4 EAS exome AF: 0.365

Gnomad4 SAS exome AF: 0.404

Gnomad4 FIN exome AF: 0.411

Gnomad4 NFE exome AF: 0.411

Gnomad4 OTH exome AF: 0.452

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

Gnomad4 AFR AF: 0.836

Gnomad4 AMR AF: 0.463

Gnomad4 ASJ AF: 0.426

Gnomad4 EAS AF: 0.397

Gnomad4 SAS AF: 0.419

Gnomad4 FIN AF: 0.431

Gnomad4 NFE AF: 0.414

Gnomad4 OTH AF: 0.502

Alfa AF: 0.419 Hom.: 8338

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

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

Other links and lift over

dbSNP: rs7674212; hg19: chr4-103988899;