rs10497435

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 0.0436 in 152,282 control chromosomes in the GnomAD database, including 183 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 0.044 ( 183 hom., cov: 32)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.868
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=-0.47).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.123 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt

Frequencies

GnomAD3 genomes
AF:
0.0436
AC:
6629
AN:
152164
Hom.:
182
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0264
Gnomad AMI
AF:
0.00110
Gnomad AMR
AF:
0.0440
Gnomad ASJ
AF:
0.0634
Gnomad EAS
AF:
0.130
Gnomad SAS
AF:
0.0645
Gnomad FIN
AF:
0.0287
Gnomad MID
AF:
0.0886
Gnomad NFE
AF:
0.0472
Gnomad OTH
AF:
0.0527
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
0.00
AC:
0
AN:
4
Hom.:
0
Cov.:
0
AF XY:
0.00
AC XY:
0
AN XY:
2
Gnomad4 NFE exome
AF:
0.00
GnomAD4 genome
AF:
0.0436
AC:
6632
AN:
152282
Hom.:
183
Cov.:
32
AF XY:
0.0432
AC XY:
3214
AN XY:
74474
show subpopulations
Gnomad4 AFR
AF:
0.0265
Gnomad4 AMR
AF:
0.0440
Gnomad4 ASJ
AF:
0.0634
Gnomad4 EAS
AF:
0.131
Gnomad4 SAS
AF:
0.0645
Gnomad4 FIN
AF:
0.0287
Gnomad4 NFE
AF:
0.0472
Gnomad4 OTH
AF:
0.0521
Alfa
AF:
0.0426
Hom.:
27
Bravo
AF:
0.0443
Asia WGS
AF:
0.114
AC:
396
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.47
CADD
Benign
9.6
DANN
Benign
0.83

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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: rs10497435; hg19: chr2-176047668; API