rs2391371

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 0.0557 in 152,266 control chromosomes in the GnomAD database, including 341 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 0.056 ( 341 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0200
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=-0.84).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.125 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:
0.0557
AC:
8472
AN:
152148
Hom.:
340
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.100
Gnomad AMI
AF:
0.00219
Gnomad AMR
AF:
0.0650
Gnomad ASJ
AF:
0.0389
Gnomad EAS
AF:
0.133
Gnomad SAS
AF:
0.0439
Gnomad FIN
AF:
0.0181
Gnomad MID
AF:
0.0759
Gnomad NFE
AF:
0.0285
Gnomad OTH
AF:
0.0627
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0557
AC:
8488
AN:
152266
Hom.:
341
Cov.:
32
AF XY:
0.0558
AC XY:
4158
AN XY:
74458
show subpopulations
Gnomad4 AFR
AF:
0.100
Gnomad4 AMR
AF:
0.0650
Gnomad4 ASJ
AF:
0.0389
Gnomad4 EAS
AF:
0.134
Gnomad4 SAS
AF:
0.0441
Gnomad4 FIN
AF:
0.0181
Gnomad4 NFE
AF:
0.0284
Gnomad4 OTH
AF:
0.0644
Alfa
AF:
0.0399
Hom.:
25
Bravo
AF:
0.0616
Asia WGS
AF:
0.0760
AC:
265
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.84
CADD
Benign
1.6
DANN
Benign
0.66

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: rs2391371; hg19: chr1-94599284; API