rs4973768
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.*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
NM_001321103.2 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.40
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 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
Ensembl
Frequencies
GnomAD3 genomes AF: 0.440 AC: 66738AN: 151730Hom.: 15122 Cov.: 33 show subpopulations
GnomAD3 genomes
AF:
AC:
66738
AN:
151730
Hom.:
Cov.:
33
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: 0.402 AC: 165AN: 410Hom.: 32 Cov.: 0 AF XY: 0.360 AC XY: 90AN XY: 250 show subpopulations
GnomAD4 exome
AF:
AC:
165
AN:
410
Hom.:
Cov.:
0
AF XY:
AC XY:
90
AN XY:
250
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:
AC:
162
AN:
404
Gnomad4 NFE exome
AF:
AC:
2
AN:
2
Gnomad4 Remaining exome
AF:
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: 66758AN: 151850Hom.: 15123 Cov.: 33 AF XY: 0.440 AC XY: 32658AN XY: 74202 show subpopulations
GnomAD4 genome
AF:
AC:
66758
AN:
151850
Hom.:
Cov.:
33
AF XY:
AC XY:
32658
AN XY:
74202
Gnomad4 AFR
AF:
AC:
0.357694
AN:
0.357694
Gnomad4 AMR
AF:
AC:
0.536823
AN:
0.536823
Gnomad4 ASJ
AF:
AC:
0.562572
AN:
0.562572
Gnomad4 EAS
AF:
AC:
0.191995
AN:
0.191995
Gnomad4 SAS
AF:
AC:
0.440994
AN:
0.440994
Gnomad4 FIN
AF:
AC:
0.447069
AN:
0.447069
Gnomad4 NFE
AF:
AC:
0.476545
AN:
0.476545
Gnomad4 OTH
AF:
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:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
1276
AN:
3472
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
Mutation Taster
=100/0
polymorphism (auto)
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