rs1863196

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 0.387 in 152,046 control chromosomes in the GnomAD database, including 12,717 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 0.39 ( 12717 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.00700
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=-0.87).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.483 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:
0.387
AC:
58847
AN:
151928
Hom.:
12710
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.202
Gnomad AMI
AF:
0.606
Gnomad AMR
AF:
0.357
Gnomad ASJ
AF:
0.466
Gnomad EAS
AF:
0.340
Gnomad SAS
AF:
0.330
Gnomad FIN
AF:
0.522
Gnomad MID
AF:
0.354
Gnomad NFE
AF:
0.487
Gnomad OTH
AF:
0.391
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.387
AC:
58867
AN:
152046
Hom.:
12717
Cov.:
32
AF XY:
0.391
AC XY:
29028
AN XY:
74318
show subpopulations
Gnomad4 AFR
AF:
0.201
Gnomad4 AMR
AF:
0.356
Gnomad4 ASJ
AF:
0.466
Gnomad4 EAS
AF:
0.341
Gnomad4 SAS
AF:
0.331
Gnomad4 FIN
AF:
0.522
Gnomad4 NFE
AF:
0.487
Gnomad4 OTH
AF:
0.394
Alfa
AF:
0.435
Hom.:
1925
Bravo
AF:
0.363
Asia WGS
AF:
0.322
AC:
1119
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.87
CADD
Benign
1.7
DANN
Benign
0.47

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: rs1863196; hg19: chr2-166557510; API