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GeneBe

rs4973768

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

2

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]

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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=-0.53).
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 UniProt
SLC4A7NM_001321103.2 linkuse as main transcriptc.*2242G>A 3_prime_UTR_variant 26/26 ENST00000454389.6

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
SLC4A7ENST00000454389.6 linkuse as main transcriptc.*2242G>A 3_prime_UTR_variant 26/261 NM_001321103.2 Q9Y6M7-7
ENST00000661166.1 linkuse as main transcriptn.975+3980C>T intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
AF:
0.440
AC:
66738
AN:
151730
Hom.:
15122
Cov.:
33
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.:
32
Cov.:
0
AF XY:
0.360
AC XY:
90
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.:
33
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
11
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.

Other links and lift over

dbSNP: rs4973768; hg19: chr3-27416013; COSMIC: COSV55394698; COSMIC: COSV55394698; API