Variant rs868884 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001039960.3(SLC4A8):c.2172+108G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.531 in 1,040,646 control chromosomes in the GnomAD database, including 148,299 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 ( 22262 hom., cov: 32)

Exomes 𝑓: 0.53 ( 126037 hom. )

Consequence

SLC4A8
NM_001039960.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.806

Variant links:

Genes affected

SLC4A8 (HGNC:11034): (solute carrier family 4 member 8) The protein encoded by this gene is a membrane protein that functions to transport sodium and bicarbonate ions across the cell membrane. The encoded protein is important for pH regulation in neurons. The activity of this protein can be inhibited by 4,4'-Di-isothiocyanatostilbene-2,2'-disulfonic acid (DIDS). Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Apr 2012]

SLC4A8 links:

SLC4A8 (HGNC:):

SLC4A8 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.88).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.57 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC4A8	NM_001039960.3 linkuse as main transcript	c.2172+108G>A		intron_variant		ENST00000453097.7	NP_001035049.1	Q2Y0W8-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC4A8	ENST00000453097.7 linkuse as main transcript	c.2172+108G>A		intron_variant		1	NM_001039960.3	ENSP00000405812.2		Q2Y0W8-1

Frequencies

GnomAD3 genomes

AF:

0.540

AC:

81964

AN:

151916

Hom.:

22253

Cov.:

show subpopulations

Gnomad AFR

AF:

0.576

Gnomad AMI

AF:

0.643

Gnomad AMR

AF:

0.472

Gnomad ASJ

AF:

0.603

Gnomad EAS

AF:

0.470

Gnomad SAS

AF:

0.534

Gnomad FIN

AF:

0.579

Gnomad MID

AF:

0.459

Gnomad NFE

AF:

0.528

Gnomad OTH

AF:

0.523

GnomAD4 exome

AF:

0.529

AC:

470303

AN:

888612

Hom.:

126037

AF XY:

0.529

AC XY:

241506

AN XY:

456930

show subpopulations

Gnomad4 AFR exome

AF:

0.579

Gnomad4 AMR exome

AF:

0.419

Gnomad4 ASJ exome

AF:

0.584

Gnomad4 EAS exome

AF:

0.485

Gnomad4 SAS exome

AF:

0.517

Gnomad4 FIN exome

AF:

0.580

Gnomad4 NFE exome

AF:

0.533

Gnomad4 OTH exome

AF:

0.528

GnomAD4 genome

AF:

0.539

AC:

82022

AN:

152034

Hom.:

22262

Cov.:

AF XY:

0.539

AC XY:

40014

AN XY:

74298

show subpopulations

Gnomad4 AFR

AF:

0.576

Gnomad4 AMR

AF:

0.471

Gnomad4 ASJ

AF:

0.603

Gnomad4 EAS

AF:

0.471

Gnomad4 SAS

AF:

0.534

Gnomad4 FIN

AF:

0.579

Gnomad4 NFE

AF:

0.528

Gnomad4 OTH

AF:

0.524

Alfa

AF:

0.536

Hom.:

3923

Bravo

AF:

0.530

Asia WGS

AF:

0.513

AC:

1786

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

0.60

DANN

Benign

0.31

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over