rs4973768

Variant summary

Our verdict is Benign. The variant received -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]

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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 rank MANE Protein UniProt
SLC4A7NM_001321103.2 linkc.*2242G>A 3_prime_UTR_variant Exon 26 of 26 ENST00000454389.6 NP_001308032.1 Q9Y6M7-7

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
SLC4A7ENST00000454389 linkc.*2242G>A 3_prime_UTR_variant Exon 26 of 26 1 NM_001321103.2 ENSP00000390394.1 Q9Y6M7-7

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 AFR exome
AC:
0
AN:
0
Gnomad4 AMR exome
AC:
0
AN:
0
Gnomad4 ASJ exome
AC:
0
AN:
0
Gnomad4 EAS exome
AC:
0
AN:
0
Gnomad4 SAS exome
AC:
0
AN:
0
Gnomad4 FIN exome
AF:
0.401
AC:
162
AN:
404
Gnomad4 NFE exome
AF:
1.00
AC:
2
AN:
2
Gnomad4 Remaining exome
AF:
0.250
AC:
1
AN:
4
Heterozygous variant carriers
0
5
10
14
19
24
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
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
AC:
0.357694
AN:
0.357694
Gnomad4 AMR
AF:
0.537
AC:
0.536823
AN:
0.536823
Gnomad4 ASJ
AF:
0.563
AC:
0.562572
AN:
0.562572
Gnomad4 EAS
AF:
0.192
AC:
0.191995
AN:
0.191995
Gnomad4 SAS
AF:
0.441
AC:
0.440994
AN:
0.440994
Gnomad4 FIN
AF:
0.447
AC:
0.447069
AN:
0.447069
Gnomad4 NFE
AF:
0.477
AC:
0.476545
AN:
0.476545
Gnomad4 OTH
AF:
0.471
AC:
0.471063
AN:
0.471063
Heterozygous variant carriers
0
1933
3866
5799
7732
9665
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Genome Het
Genome Hom
Variant carriers
0
632
1264
1896
2528
3160
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
0.467
Hom.:
78340
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
Mutation Taster
=100/0
polymorphism (auto)

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