chr3-27433860-G-A
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001321103.2(SLC4A7):c.778+56C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.118 in 1,413,372 control chromosomes in the GnomAD database, including 10,596 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 0.13 ( 1215 hom., cov: 32)
Exomes 𝑓: 0.12 ( 9381 hom. )
Consequence
SLC4A7
NM_001321103.2 intron
NM_001321103.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.05
Publications
10 publications found
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 Gene-Disease associations (from GenCC):
- cone-rod dystrophyInheritance: AR Classification: LIMITED Submitted by: Franklin by Genoox
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=-0.83).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.139 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.127 AC: 19252AN: 152030Hom.: 1215 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
19252
AN:
152030
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.118 AC: 148218AN: 1261222Hom.: 9381 AF XY: 0.116 AC XY: 73700AN XY: 638018 show subpopulations
GnomAD4 exome
AF:
AC:
148218
AN:
1261222
Hom.:
AF XY:
AC XY:
73700
AN XY:
638018
show subpopulations
African (AFR)
AF:
AC:
4153
AN:
29098
American (AMR)
AF:
AC:
4102
AN:
43102
Ashkenazi Jewish (ASJ)
AF:
AC:
4024
AN:
24812
East Asian (EAS)
AF:
AC:
2421
AN:
38698
South Asian (SAS)
AF:
AC:
3433
AN:
81106
European-Finnish (FIN)
AF:
AC:
5225
AN:
53054
Middle Eastern (MID)
AF:
AC:
1093
AN:
5362
European-Non Finnish (NFE)
AF:
AC:
117028
AN:
932360
Other (OTH)
AF:
AC:
6739
AN:
53630
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.501
Heterozygous variant carriers
0
6555
13110
19665
26220
32775
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome AF: 0.127 AC: 19249AN: 152150Hom.: 1215 Cov.: 32 AF XY: 0.124 AC XY: 9248AN XY: 74356 show subpopulations
GnomAD4 genome
AF:
AC:
19249
AN:
152150
Hom.:
Cov.:
32
AF XY:
AC XY:
9248
AN XY:
74356
show subpopulations
African (AFR)
AF:
AC:
5914
AN:
41528
American (AMR)
AF:
AC:
1831
AN:
15282
Ashkenazi Jewish (ASJ)
AF:
AC:
567
AN:
3472
East Asian (EAS)
AF:
AC:
277
AN:
5160
South Asian (SAS)
AF:
AC:
230
AN:
4826
European-Finnish (FIN)
AF:
AC:
1040
AN:
10574
Middle Eastern (MID)
AF:
AC:
56
AN:
294
European-Non Finnish (NFE)
AF:
AC:
8890
AN:
67996
Other (OTH)
AF:
AC:
284
AN:
2106
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.503
Heterozygous variant carriers
0
872
1744
2617
3489
4361
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
282
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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