2-161863591-T-G

Position:

• chr2-161863591-T-G

Variant summary

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

The NM_001178015.2(SLC4A10):​c.766+529T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.595 in 152,076 control chromosomes in the GnomAD database, including 27,098 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 0.60 (27098 hom., cov: 32)
• Consequence: SLC4A10 NM_001178015.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.289

Genes affected

SLC4A10 (HGNC:13811): (solute carrier family 4 member 10) This gene belongs to a small family of sodium-coupled bicarbonate transporters (NCBTs) that regulate the intracellular pH of neurons, the secretion of bicarbonate ions across the choroid plexus, and the pH of the brain extracellular fluid. The protein encoded by this gene was initially identified as a sodium-driven chloride bicarbonate exchanger (NCBE) though there is now evidence that its sodium/bicarbonate cotransport activity is independent of any chloride ion countertransport under physiological conditions. This gene is now classified as a member A10 of the SLC4 family of transmembrane solute carriers. Alternative splicing results in multiple transcript variants encoding distinct isoforms.[provided by RefSeq, May 2010]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.83 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC4A10	NM_001178015.2	c.766+529T>G		intron_variant		ENST00000446997.6	NP_001171486.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC4A10	ENST00000446997.6	c.766+529T>G		intron_variant		1	NM_001178015.2	ENSP00000393066	P4

Frequencies

GnomAD3 genomes AF: 0.595 AC: 90466 AN: 151958 Hom.: 27089 Cov.: 32

Gnomad AFR AF: 0.578

Gnomad AMI AF: 0.520

Gnomad AMR AF: 0.527

Gnomad ASJ AF: 0.631

Gnomad EAS AF: 0.851

Gnomad SAS AF: 0.554

Gnomad FIN AF: 0.600

Gnomad MID AF: 0.620

Gnomad NFE AF: 0.604

Gnomad OTH AF: 0.583

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

GnomAD4 genome AF: 0.595 AC: 90505 AN: 152076 Hom.: 27098 Cov.: 32 AF XY: 0.594 AC XY: 44176 AN XY: 74368

Gnomad4 AFR AF: 0.577

Gnomad4 AMR AF: 0.527

Gnomad4 ASJ AF: 0.631

Gnomad4 EAS AF: 0.851

Gnomad4 SAS AF: 0.553

Gnomad4 FIN AF: 0.600

Gnomad4 NFE AF: 0.604

Gnomad4 OTH AF: 0.584

Alfa AF: 0.593 Hom.: 35200

Bravo AF: 0.589

Asia WGS AF: 0.681 AC: 2368 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	2.1
DANN	Benign	0.72

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: rs1227929; hg19: chr2-162720101;