NM_003040.4:c.1147+95G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_003040.4(SLC4A2):​c.1147+95G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.189 in 961,352 control chromosomes in the GnomAD database, including 19,075 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 0.15 ( 2078 hom., cov: 33)
Exomes 𝑓: 0.20 ( 16997 hom. )

Consequence

SLC4A2
NM_003040.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.395

Publications

5 publications found
Variant links:
Genes affected
SLC4A2 (HGNC:11028): (solute carrier family 4 member 2) This gene encodes a member of the anion exchanger family of membrane transport proteins. The encoded protein regulates intracellular pH, biliary bicarbonate secretion, and chloride uptake. Reduced expression of this gene may be associated with primary biliary cirrhosis (PBC) in human patients, while differential expression of this gene may be associated with malignant hepatocellular carcinoma, colon and gastric cancers. [provided by RefSeq, Nov 2016]

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=-0.9).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.258 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
SLC4A2NM_003040.4 linkc.1147+95G>A intron_variant Intron 8 of 22 ENST00000413384.7 NP_003031.3 P04920-1
SLC4A2NM_001199692.3 linkc.1147+95G>A intron_variant Intron 8 of 22 NP_001186621.1 P04920-1Q59GF1
SLC4A2NM_001199693.1 linkc.1120+95G>A intron_variant Intron 7 of 21 NP_001186622.1 P04920-3Q59GF1
SLC4A2NM_001199694.2 linkc.1105+95G>A intron_variant Intron 7 of 21 NP_001186623.1 P04920-2Q59GF1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
SLC4A2ENST00000413384.7 linkc.1147+95G>A intron_variant Intron 8 of 22 1 NM_003040.4 ENSP00000405600.2 P04920-1

Frequencies

GnomAD3 genomes
AF:
0.154
AC:
23419
AN:
152098
Hom.:
2078
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.0886
Gnomad AMI
AF:
0.0515
Gnomad AMR
AF:
0.126
Gnomad ASJ
AF:
0.164
Gnomad EAS
AF:
0.0200
Gnomad SAS
AF:
0.271
Gnomad FIN
AF:
0.134
Gnomad MID
AF:
0.206
Gnomad NFE
AF:
0.206
Gnomad OTH
AF:
0.158
GnomAD4 exome
AF:
0.196
AC:
158644
AN:
809136
Hom.:
16997
AF XY:
0.198
AC XY:
79303
AN XY:
399806
show subpopulations
African (AFR)
AF:
0.0817
AC:
1361
AN:
16660
American (AMR)
AF:
0.109
AC:
1091
AN:
9980
Ashkenazi Jewish (ASJ)
AF:
0.161
AC:
2413
AN:
14950
East Asian (EAS)
AF:
0.0235
AC:
620
AN:
26436
South Asian (SAS)
AF:
0.266
AC:
10809
AN:
40560
European-Finnish (FIN)
AF:
0.144
AC:
4473
AN:
30990
Middle Eastern (MID)
AF:
0.190
AC:
565
AN:
2968
European-Non Finnish (NFE)
AF:
0.207
AC:
130459
AN:
629334
Other (OTH)
AF:
0.184
AC:
6853
AN:
37258
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.504
Heterozygous variant carriers
0
6180
12359
18539
24718
30898
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Exome Het
Exome Hom
Variant carriers
0
3962
7924
11886
15848
19810
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome
AF:
0.154
AC:
23430
AN:
152216
Hom.:
2078
Cov.:
33
AF XY:
0.150
AC XY:
11143
AN XY:
74400
show subpopulations
African (AFR)
AF:
0.0886
AC:
3681
AN:
41550
American (AMR)
AF:
0.126
AC:
1923
AN:
15304
Ashkenazi Jewish (ASJ)
AF:
0.164
AC:
568
AN:
3464
East Asian (EAS)
AF:
0.0201
AC:
104
AN:
5186
South Asian (SAS)
AF:
0.270
AC:
1302
AN:
4824
European-Finnish (FIN)
AF:
0.134
AC:
1417
AN:
10566
Middle Eastern (MID)
AF:
0.204
AC:
60
AN:
294
European-Non Finnish (NFE)
AF:
0.206
AC:
13989
AN:
68000
Other (OTH)
AF:
0.160
AC:
339
AN:
2116
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.496
Heterozygous variant carriers
0
998
1996
2993
3991
4989
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
282
564
846
1128
1410
<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:
0.173
Hom.:
3178
Bravo
AF:
0.145
Asia WGS
AF:
0.157
AC:
548
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
0.76
DANN
Benign
0.68
PhyloP100
-0.40
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.1
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

Other links and lift over

dbSNP: rs12703112; hg19: chr7-150765236; API