rs10205049

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 0.483 in 151,904 control chromosomes in the GnomAD database, including 18,584 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 0.48 ( 18584 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.128
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=-0.92).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.565 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:
0.483
AC:
73264
AN:
151786
Hom.:
18579
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.365
Gnomad AMI
AF:
0.360
Gnomad AMR
AF:
0.521
Gnomad ASJ
AF:
0.528
Gnomad EAS
AF:
0.139
Gnomad SAS
AF:
0.465
Gnomad FIN
AF:
0.501
Gnomad MID
AF:
0.453
Gnomad NFE
AF:
0.570
Gnomad OTH
AF:
0.475
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.483
AC:
73296
AN:
151904
Hom.:
18584
Cov.:
32
AF XY:
0.478
AC XY:
35498
AN XY:
74222
show subpopulations
Gnomad4 AFR
AF:
0.364
Gnomad4 AMR
AF:
0.522
Gnomad4 ASJ
AF:
0.528
Gnomad4 EAS
AF:
0.138
Gnomad4 SAS
AF:
0.466
Gnomad4 FIN
AF:
0.501
Gnomad4 NFE
AF:
0.570
Gnomad4 OTH
AF:
0.473
Alfa
AF:
0.545
Hom.:
24215
Bravo
AF:
0.474
Asia WGS
AF:
0.304
AC:
1060
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.92
CADD
Benign
3.6
DANN
Benign
0.55

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: rs10205049; hg19: chr2-119899933; COSMIC: COSV60101441; API