rs7496492

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 0.0639 in 151,744 control chromosomes in the GnomAD database, including 909 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 0.064 ( 909 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0810
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=-0.95).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.202 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:
0.0636
AC:
9644
AN:
151626
Hom.:
891
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.205
Gnomad AMI
AF:
0.00219
Gnomad AMR
AF:
0.0295
Gnomad ASJ
AF:
0.0265
Gnomad EAS
AF:
0.0121
Gnomad SAS
AF:
0.00665
Gnomad FIN
AF:
0.00284
Gnomad MID
AF:
0.0443
Gnomad NFE
AF:
0.00605
Gnomad OTH
AF:
0.0465
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0639
AC:
9703
AN:
151744
Hom.:
909
Cov.:
32
AF XY:
0.0617
AC XY:
4577
AN XY:
74142
show subpopulations
Gnomad4 AFR
AF:
0.206
Gnomad4 AMR
AF:
0.0294
Gnomad4 ASJ
AF:
0.0265
Gnomad4 EAS
AF:
0.0121
Gnomad4 SAS
AF:
0.00644
Gnomad4 FIN
AF:
0.00284
Gnomad4 NFE
AF:
0.00605
Gnomad4 OTH
AF:
0.0484
Alfa
AF:
0.0445
Hom.:
84
Bravo
AF:
0.0721
Asia WGS
AF:
0.0510
AC:
176
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.95
CADD
Benign
3.2
DANN
Benign
0.69

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: rs7496492; hg19: chr15-55244650; API