rs1395087

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 0.134 in 151,752 control chromosomes in the GnomAD database, including 1,443 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 0.13 ( 1443 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.255
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=-0.89).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.16 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:
0.134
AC:
20390
AN:
151638
Hom.:
1443
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0913
Gnomad AMI
AF:
0.127
Gnomad AMR
AF:
0.135
Gnomad ASJ
AF:
0.124
Gnomad EAS
AF:
0.108
Gnomad SAS
AF:
0.169
Gnomad FIN
AF:
0.154
Gnomad MID
AF:
0.272
Gnomad NFE
AF:
0.157
Gnomad OTH
AF:
0.141
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.134
AC:
20392
AN:
151752
Hom.:
1443
Cov.:
32
AF XY:
0.137
AC XY:
10145
AN XY:
74156
show subpopulations
Gnomad4 AFR
AF:
0.0913
Gnomad4 AMR
AF:
0.135
Gnomad4 ASJ
AF:
0.124
Gnomad4 EAS
AF:
0.108
Gnomad4 SAS
AF:
0.169
Gnomad4 FIN
AF:
0.154
Gnomad4 NFE
AF:
0.157
Gnomad4 OTH
AF:
0.140
Alfa
AF:
0.153
Hom.:
749
Bravo
AF:
0.128
Asia WGS
AF:
0.130
AC:
450
AN:
3460

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
CADD
Benign
4.8
DANN
Benign
0.76

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: rs1395087; hg19: chr21-24528815; API