rs1695508

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 0.249 in 152,074 control chromosomes in the GnomAD database, including 5,067 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 0.25 ( 5067 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.240
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=-0.83).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.586 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:
0.249
AC:
37816
AN:
151956
Hom.:
5061
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.260
Gnomad AMI
AF:
0.248
Gnomad AMR
AF:
0.277
Gnomad ASJ
AF:
0.288
Gnomad EAS
AF:
0.606
Gnomad SAS
AF:
0.254
Gnomad FIN
AF:
0.256
Gnomad MID
AF:
0.225
Gnomad NFE
AF:
0.205
Gnomad OTH
AF:
0.236
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.249
AC:
37856
AN:
152074
Hom.:
5067
Cov.:
32
AF XY:
0.254
AC XY:
18851
AN XY:
74320
show subpopulations
Gnomad4 AFR
AF:
0.261
Gnomad4 AMR
AF:
0.277
Gnomad4 ASJ
AF:
0.288
Gnomad4 EAS
AF:
0.604
Gnomad4 SAS
AF:
0.255
Gnomad4 FIN
AF:
0.256
Gnomad4 NFE
AF:
0.205
Gnomad4 OTH
AF:
0.241
Alfa
AF:
0.228
Hom.:
509
Bravo
AF:
0.254
Asia WGS
AF:
0.402
AC:
1395
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.83
CADD
Benign
6.3
DANN
Benign
0.78

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: rs1695508; hg19: chr7-28966556; API