chr15-101267710-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The variant allele was found at a frequency of 0.192 in 152,202 control chromosomes in the GnomAD database, including 3,647 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 0.19 ( 3647 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.818
Variant links:

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ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.255 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt

Frequencies

GnomAD3 genomes
AF:
0.192
AC:
29217
AN:
152086
Hom.:
3646
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0459
Gnomad AMI
AF:
0.488
Gnomad AMR
AF:
0.195
Gnomad ASJ
AF:
0.234
Gnomad EAS
AF:
0.169
Gnomad SAS
AF:
0.171
Gnomad FIN
AF:
0.323
Gnomad MID
AF:
0.171
Gnomad NFE
AF:
0.258
Gnomad OTH
AF:
0.185
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.192
AC:
29221
AN:
152202
Hom.:
3647
Cov.:
32
AF XY:
0.194
AC XY:
14440
AN XY:
74402
show subpopulations
Gnomad4 AFR
AF:
0.0457
Gnomad4 AMR
AF:
0.196
Gnomad4 ASJ
AF:
0.234
Gnomad4 EAS
AF:
0.169
Gnomad4 SAS
AF:
0.171
Gnomad4 FIN
AF:
0.323
Gnomad4 NFE
AF:
0.258
Gnomad4 OTH
AF:
0.183
Alfa
AF:
0.229
Hom.:
5747
Bravo
AF:
0.178
Asia WGS
AF:
0.143
AC:
498
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.88
CADD
Benign
5.7
DANN
Benign
0.74

Splicing

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: rs2101171; hg19: chr15-101807915; API