rs1595963

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 0.041 in 152,134 control chromosomes in the GnomAD database, including 189 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 0.041 ( 189 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.252
Variant links:

Genome browser will be placed here

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0837 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:
0.0410
AC:
6228
AN:
152016
Hom.:
187
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0695
Gnomad AMI
AF:
0.0132
Gnomad AMR
AF:
0.0462
Gnomad ASJ
AF:
0.0181
Gnomad EAS
AF:
0.0903
Gnomad SAS
AF:
0.0315
Gnomad FIN
AF:
0.0174
Gnomad MID
AF:
0.0348
Gnomad NFE
AF:
0.0248
Gnomad OTH
AF:
0.0363
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0410
AC:
6240
AN:
152134
Hom.:
189
Cov.:
32
AF XY:
0.0406
AC XY:
3018
AN XY:
74350
show subpopulations
Gnomad4 AFR
AF:
0.0695
Gnomad4 AMR
AF:
0.0462
Gnomad4 ASJ
AF:
0.0181
Gnomad4 EAS
AF:
0.0905
Gnomad4 SAS
AF:
0.0311
Gnomad4 FIN
AF:
0.0174
Gnomad4 NFE
AF:
0.0248
Gnomad4 OTH
AF:
0.0378
Alfa
AF:
0.0314
Hom.:
22
Bravo
AF:
0.0462
Asia WGS
AF:
0.0720
AC:
252
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
6.2
DANN
Benign
0.52

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: rs1595963; hg19: chr18-27460348; API