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GeneBe

rs1799964

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 0.196 in 151,164 control chromosomes in the GnomAD database, including 2,988 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 0.20 ( 2988 hom., cov: 30)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.13
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 (SAS) allele frequency at 95% confidence interval = 0.311 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:
0.196
AC:
29605
AN:
151046
Hom.:
2988
Cov.:
30
show subpopulations
Gnomad AFR
AF:
0.161
Gnomad AMI
AF:
0.184
Gnomad AMR
AF:
0.193
Gnomad ASJ
AF:
0.219
Gnomad EAS
AF:
0.191
Gnomad SAS
AF:
0.326
Gnomad FIN
AF:
0.178
Gnomad MID
AF:
0.203
Gnomad NFE
AF:
0.209
Gnomad OTH
AF:
0.236
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.196
AC:
29631
AN:
151164
Hom.:
2988
Cov.:
30
AF XY:
0.197
AC XY:
14541
AN XY:
73770
show subpopulations
Gnomad4 AFR
AF:
0.162
Gnomad4 AMR
AF:
0.193
Gnomad4 ASJ
AF:
0.219
Gnomad4 EAS
AF:
0.191
Gnomad4 SAS
AF:
0.324
Gnomad4 FIN
AF:
0.178
Gnomad4 NFE
AF:
0.209
Gnomad4 OTH
AF:
0.236
Alfa
AF:
0.211
Hom.:
5947
Bravo
AF:
0.194
Asia WGS
AF:
0.275
AC:
954
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
4.6
Dann
Benign
0.55

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: rs1799964; hg19: chr6-31542308; API