1-111017226-G-T

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 0.208 in 152,052 control chromosomes in the GnomAD database, including 3,542 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 0.21 ( 3542 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.347
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=-0.8).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.25 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt

Frequencies

GnomAD3 genomes
AF:
0.208
AC:
31640
AN:
151934
Hom.:
3543
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.165
Gnomad AMI
AF:
0.167
Gnomad AMR
AF:
0.167
Gnomad ASJ
AF:
0.248
Gnomad EAS
AF:
0.00404
Gnomad SAS
AF:
0.169
Gnomad FIN
AF:
0.258
Gnomad MID
AF:
0.247
Gnomad NFE
AF:
0.253
Gnomad OTH
AF:
0.208
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.208
AC:
31651
AN:
152052
Hom.:
3542
Cov.:
32
AF XY:
0.204
AC XY:
15137
AN XY:
74332
show subpopulations
Gnomad4 AFR
AF:
0.164
Gnomad4 AMR
AF:
0.167
Gnomad4 ASJ
AF:
0.248
Gnomad4 EAS
AF:
0.00405
Gnomad4 SAS
AF:
0.170
Gnomad4 FIN
AF:
0.258
Gnomad4 NFE
AF:
0.253
Gnomad4 OTH
AF:
0.205
Alfa
AF:
0.234
Hom.:
6248
Bravo
AF:
0.197
Asia WGS
AF:
0.0880
AC:
305
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.80
CADD
Benign
2.0
DANN
Benign
0.68

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: rs12735344; hg19: chr1-111559848; API