rs847964

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 0.102 in 151,942 control chromosomes in the GnomAD database, including 985 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 0.10 ( 985 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.69
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=-1.05).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.173 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:
0.102
AC:
15540
AN:
151824
Hom.:
978
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.176
Gnomad AMI
AF:
0.225
Gnomad AMR
AF:
0.0845
Gnomad ASJ
AF:
0.0943
Gnomad EAS
AF:
0.0615
Gnomad SAS
AF:
0.0426
Gnomad FIN
AF:
0.0389
Gnomad MID
AF:
0.114
Gnomad NFE
AF:
0.0773
Gnomad OTH
AF:
0.104
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.102
AC:
15568
AN:
151942
Hom.:
985
Cov.:
32
AF XY:
0.0996
AC XY:
7392
AN XY:
74248
show subpopulations
Gnomad4 AFR
AF:
0.177
Gnomad4 AMR
AF:
0.0843
Gnomad4 ASJ
AF:
0.0943
Gnomad4 EAS
AF:
0.0613
Gnomad4 SAS
AF:
0.0424
Gnomad4 FIN
AF:
0.0389
Gnomad4 NFE
AF:
0.0773
Gnomad4 OTH
AF:
0.103
Alfa
AF:
0.0897
Hom.:
89
Bravo
AF:
0.111
Asia WGS
AF:
0.0620
AC:
216
AN:
3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.1
CADD
Benign
0.12
DANN
Benign
0.085

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: rs847964; hg19: chr7-12493457; API