rs1609717

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 0.951 in 152,208 control chromosomes in the GnomAD database, including 68,927 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 0.95 ( 68927 hom., cov: 33)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.00
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=-0.91).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.953 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt

Frequencies

GnomAD3 genomes
AF:
0.951
AC:
144713
AN:
152090
Hom.:
68878
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.958
Gnomad AMI
AF:
0.985
Gnomad AMR
AF:
0.962
Gnomad ASJ
AF:
0.952
Gnomad EAS
AF:
0.976
Gnomad SAS
AF:
0.901
Gnomad FIN
AF:
0.945
Gnomad MID
AF:
0.943
Gnomad NFE
AF:
0.947
Gnomad OTH
AF:
0.953
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.951
AC:
144820
AN:
152208
Hom.:
68927
Cov.:
33
AF XY:
0.950
AC XY:
70738
AN XY:
74426
show subpopulations
Gnomad4 AFR
AF:
0.958
Gnomad4 AMR
AF:
0.962
Gnomad4 ASJ
AF:
0.952
Gnomad4 EAS
AF:
0.976
Gnomad4 SAS
AF:
0.900
Gnomad4 FIN
AF:
0.945
Gnomad4 NFE
AF:
0.947
Gnomad4 OTH
AF:
0.954
Alfa
AF:
0.949
Hom.:
8503
Bravo
AF:
0.956
Asia WGS
AF:
0.943
AC:
3280
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
0.039
DANN
Benign
0.53

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: rs1609717; hg19: chr19-4519450; API