1-91123257-A-G

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 0.414 in 152,050 control chromosomes in the GnomAD database, including 13,317 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 0.41 ( 13317 hom., cov: 33)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.19
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=-0.92).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.468 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:
0.414
AC:
62967
AN:
151934
Hom.:
13304
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.474
Gnomad AMI
AF:
0.176
Gnomad AMR
AF:
0.393
Gnomad ASJ
AF:
0.339
Gnomad EAS
AF:
0.473
Gnomad SAS
AF:
0.385
Gnomad FIN
AF:
0.450
Gnomad MID
AF:
0.392
Gnomad NFE
AF:
0.382
Gnomad OTH
AF:
0.411
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.414
AC:
63005
AN:
152050
Hom.:
13317
Cov.:
33
AF XY:
0.417
AC XY:
30968
AN XY:
74318
show subpopulations
Gnomad4 AFR
AF:
0.474
Gnomad4 AMR
AF:
0.393
Gnomad4 ASJ
AF:
0.339
Gnomad4 EAS
AF:
0.472
Gnomad4 SAS
AF:
0.385
Gnomad4 FIN
AF:
0.450
Gnomad4 NFE
AF:
0.383
Gnomad4 OTH
AF:
0.407
Alfa
AF:
0.394
Hom.:
5638
Bravo
AF:
0.417
Asia WGS
AF:
0.404
AC:
1406
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.92
CADD
Benign
0.14
DANN
Benign
0.23

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: rs346981; hg19: chr1-91588814; API