chr1-198626376-G-A

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 0.0691 in 152,200 control chromosomes in the GnomAD database, including 476 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 0.069 ( 476 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.21
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=-1.0).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.145 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:
0.0692
AC:
10525
AN:
152082
Hom.:
478
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0169
Gnomad AMI
AF:
0.0702
Gnomad AMR
AF:
0.108
Gnomad ASJ
AF:
0.0794
Gnomad EAS
AF:
0.154
Gnomad SAS
AF:
0.120
Gnomad FIN
AF:
0.114
Gnomad MID
AF:
0.120
Gnomad NFE
AF:
0.0747
Gnomad OTH
AF:
0.0687
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0691
AC:
10523
AN:
152200
Hom.:
476
Cov.:
32
AF XY:
0.0742
AC XY:
5517
AN XY:
74396
show subpopulations
Gnomad4 AFR
AF:
0.0169
Gnomad4 AMR
AF:
0.108
Gnomad4 ASJ
AF:
0.0794
Gnomad4 EAS
AF:
0.154
Gnomad4 SAS
AF:
0.120
Gnomad4 FIN
AF:
0.114
Gnomad4 NFE
AF:
0.0747
Gnomad4 OTH
AF:
0.0680
Alfa
AF:
0.0724
Hom.:
564
Bravo
AF:
0.0661
Asia WGS
AF:
0.132
AC:
457
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
0.15
DANN
Benign
0.65

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: rs12127588; hg19: chr1-198595506; API