rs10497015

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 0.339 in 151,662 control chromosomes in the GnomAD database, including 9,020 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 0.34 ( 9020 hom., cov: 30)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.203
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=-0.85).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.386 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:
0.339
AC:
51433
AN:
151544
Hom.:
9024
Cov.:
30
show subpopulations
Gnomad AFR
AF:
0.279
Gnomad AMI
AF:
0.379
Gnomad AMR
AF:
0.285
Gnomad ASJ
AF:
0.455
Gnomad EAS
AF:
0.232
Gnomad SAS
AF:
0.295
Gnomad FIN
AF:
0.347
Gnomad MID
AF:
0.528
Gnomad NFE
AF:
0.390
Gnomad OTH
AF:
0.375
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.339
AC:
51428
AN:
151662
Hom.:
9020
Cov.:
30
AF XY:
0.337
AC XY:
24950
AN XY:
74108
show subpopulations
Gnomad4 AFR
AF:
0.279
Gnomad4 AMR
AF:
0.284
Gnomad4 ASJ
AF:
0.455
Gnomad4 EAS
AF:
0.231
Gnomad4 SAS
AF:
0.295
Gnomad4 FIN
AF:
0.347
Gnomad4 NFE
AF:
0.390
Gnomad4 OTH
AF:
0.372
Alfa
AF:
0.373
Hom.:
2633
Bravo
AF:
0.334
Asia WGS
AF:
0.249
AC:
865
AN:
3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.85
CADD
Benign
9.3
DANN
Benign
0.63

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: rs10497015; hg19: chr2-148378069; API