Variant rs4973768 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_001321103.2(SLC4A7):c.*2242G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.44 in 152,260 control chromosomes in the GnomAD database, including 15,155 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 0.44 ( 15123 hom., cov: 33)

Exomes 𝑓: 0.40 ( 32 hom. )

Consequence

SLC4A7
NM_001321103.2 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.40

Variant links:

Genes affected

SLC4A7 (HGNC:11033): (solute carrier family 4 member 7) This locus encodes a sodium bicarbonate cotransporter. The encoded transmembrane protein appears to transport sodium and bicarbonate ions in a 1:1 ratio, and is thus considered an electroneutral cotransporter. The encoded protein likely plays a critical role in regulation of intracellular pH involved in visual and auditory sensory transmission. Alternatively spliced transcript variants encoding distinct isoforms have been described. [provided by RefSeq, Apr 2012]

SLC4A7 links:

(HGNC:):

links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.53).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.527 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC4A7	NM_001321103.2 linkuse as main transcript	c.*2242G>A		3_prime_UTR_variant	26/26	ENST00000454389.6	NP_001308032.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC4A7	ENST00000454389.6 linkuse as main transcript	c.*2242G>A		3_prime_UTR_variant	26/26	1	NM_001321103.2	ENSP00000390394		Q9Y6M7-7
	ENST00000661166.1 linkuse as main transcript	n.975+3980C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes

AF:

0.440

AC:

66738

AN:

151730

Hom.:

15122

Cov.:

show subpopulations

Gnomad AFR

AF:

0.358

Gnomad AMI

AF:

0.523

Gnomad AMR

AF:

0.537

Gnomad ASJ

AF:

0.563

Gnomad EAS

AF:

0.192

Gnomad SAS

AF:

0.441

Gnomad FIN

AF:

0.447

Gnomad MID

AF:

0.583

Gnomad NFE

AF:

0.476

Gnomad OTH

AF:

0.477

GnomAD4 exome

AF:

0.402

AC:

165

AN:

410

Hom.:

Cov.:

AF XY:

0.360

AC XY:

AN XY:

250

show subpopulations

Gnomad4 FIN exome

AF:

0.401

Gnomad4 NFE exome

AF:

1.00

Gnomad4 OTH exome

AF:

0.250

GnomAD4 genome

AF:

0.440

AC:

66758

AN:

151850

Hom.:

15123

Cov.:

AF XY:

0.440

AC XY:

32658

AN XY:

74202

show subpopulations

Gnomad4 AFR

AF:

0.358

Gnomad4 AMR

AF:

0.537

Gnomad4 ASJ

AF:

0.563

Gnomad4 EAS

AF:

0.192

Gnomad4 SAS

AF:

0.441

Gnomad4 FIN

AF:

0.447

Gnomad4 NFE

AF:

0.477

Gnomad4 OTH

AF:

0.471

Alfa

AF:

0.475

Hom.:

40128

Bravo

AF:

0.444

Asia WGS

AF:

0.368

AC:

1276

AN:

3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.53

CADD

Benign

DANN

Benign

0.85

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