rs1481279

Positions:

• chr4-103056781-T-A
• chr4-103056781-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_178833.7(SLC9B2):​c.442+1020A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.503 in 152,082 control chromosomes in the GnomAD database, including 21,359 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 0.50 (21359 hom., cov: 32)
• Consequence: SLC9B2 NM_178833.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0240

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=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.763 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC9B2	NM_178833.7	c.442+1020A>T		intron_variant		ENST00000394785.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC9B2	ENST00000394785.9	c.442+1020A>T		intron_variant		2	NM_178833.7	P1

Frequencies

GnomAD3 genomes AF: 0.503 AC: 76458 AN: 151964 Hom.: 21314 Cov.: 32

Gnomad AFR AF: 0.770

Gnomad AMI AF: 0.326

Gnomad AMR AF: 0.443

Gnomad ASJ AF: 0.420

Gnomad EAS AF: 0.395

Gnomad SAS AF: 0.407

Gnomad FIN AF: 0.419

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.390

Gnomad OTH AF: 0.481

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.503 AC: 76565 AN: 152082 Hom.: 21359 Cov.: 32 AF XY: 0.501 AC XY: 37250 AN XY: 74354

Gnomad4 AFR AF: 0.770

Gnomad4 AMR AF: 0.443

Gnomad4 ASJ AF: 0.420

Gnomad4 EAS AF: 0.396

Gnomad4 SAS AF: 0.408

Gnomad4 FIN AF: 0.419

Gnomad4 NFE AF: 0.390

Gnomad4 OTH AF: 0.477

Alfa AF: 0.467 Hom.: 2179

Bravo AF: 0.518

Asia WGS AF: 0.432 AC: 1502 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.3
DANN	Benign	0.18

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: rs1481279; hg19: chr4-103977938; COSMIC: COSV60019596; COSMIC: COSV60019596;