rs2395162

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 0.127 in 152,064 control chromosomes in the GnomAD database, including 1,507 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 ( 1507 hom., cov: 31)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.992
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=-0.82).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.168 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:
0.127
AC:
19345
AN:
151946
Hom.:
1507
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.0667
Gnomad AMI
AF:
0.104
Gnomad AMR
AF:
0.112
Gnomad ASJ
AF:
0.0893
Gnomad EAS
AF:
0.0395
Gnomad SAS
AF:
0.0454
Gnomad FIN
AF:
0.204
Gnomad MID
AF:
0.0506
Gnomad NFE
AF:
0.171
Gnomad OTH
AF:
0.122
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.127
AC:
19351
AN:
152064
Hom.:
1507
Cov.:
31
AF XY:
0.124
AC XY:
9244
AN XY:
74332
show subpopulations
Gnomad4 AFR
AF:
0.0669
Gnomad4 AMR
AF:
0.112
Gnomad4 ASJ
AF:
0.0893
Gnomad4 EAS
AF:
0.0394
Gnomad4 SAS
AF:
0.0448
Gnomad4 FIN
AF:
0.204
Gnomad4 NFE
AF:
0.171
Gnomad4 OTH
AF:
0.121
Alfa
AF:
0.157
Hom.:
1294
Bravo
AF:
0.119
Asia WGS
AF:
0.0570
AC:
197
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.82
CADD
Benign
0.74
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: rs2395162; hg19: chr6-32387780; API