GeneBe

12-26992864-T-C

Variant names:

Variant summary

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

The NM_016551.3(TM7SF3):​c.691-2237A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.226 in 151,222 control chromosomes in the GnomAD database, including 4,090 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 0.23 ( 4090 hom., cov: 30)

Consequence

TM7SF3
NM_016551.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.667

Publications

3 publications found
Variant links:
Genes affected
TM7SF3 (HGNC:23049): (transmembrane 7 superfamily member 3) Involved in cellular response to unfolded protein; negative regulation of programmed cell death; and positive regulation of insulin secretion. Located in plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

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=-0.76).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.366 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
TM7SF3NM_016551.3 linkc.691-2237A>G intron_variant Intron 5 of 11 ENST00000343028.9 NP_057635.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
TM7SF3ENST00000343028.9 linkc.691-2237A>G intron_variant Intron 5 of 11 1 NM_016551.3 ENSP00000342322.4

Frequencies

GnomAD3 genomes
AF:
0.226
AC:
34227
AN:
151116
Hom.:
4087
Cov.:
30
show subpopulations
Gnomad AFR
AF:
0.269
Gnomad AMI
AF:
0.282
Gnomad AMR
AF:
0.206
Gnomad ASJ
AF:
0.186
Gnomad EAS
AF:
0.379
Gnomad SAS
AF:
0.291
Gnomad FIN
AF:
0.238
Gnomad MID
AF:
0.222
Gnomad NFE
AF:
0.189
Gnomad OTH
AF:
0.216
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.226
AC:
34240
AN:
151222
Hom.:
4090
Cov.:
30
AF XY:
0.229
AC XY:
16886
AN XY:
73880
show subpopulations
African (AFR)
AF:
0.269
AC:
11048
AN:
41122
American (AMR)
AF:
0.206
AC:
3130
AN:
15178
Ashkenazi Jewish (ASJ)
AF:
0.186
AC:
644
AN:
3464
East Asian (EAS)
AF:
0.380
AC:
1948
AN:
5124
South Asian (SAS)
AF:
0.290
AC:
1393
AN:
4802
European-Finnish (FIN)
AF:
0.238
AC:
2460
AN:
10332
Middle Eastern (MID)
AF:
0.233
AC:
68
AN:
292
European-Non Finnish (NFE)
AF:
0.189
AC:
12836
AN:
67900
Other (OTH)
AF:
0.218
AC:
456
AN:
2096
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.502
Heterozygous variant carriers
0
1284
2568
3852
5136
6420
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
362
724
1086
1448
1810
<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:
0.205
Hom.:
530
Bravo
AF:
0.226
Asia WGS
AF:
0.319
AC:
1108
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.76
CADD
Benign
6.2
DANN
Benign
0.80
PhyloP100
0.67
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: rs1552257; hg19: chr12-27145797; API