rs10484676

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 0.088 in 152,288 control chromosomes in the GnomAD database, including 607 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 0.088 ( 607 hom., cov: 33)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.11
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=-0.89).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.107 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:
0.0880
AC:
13392
AN:
152170
Hom.:
608
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.110
Gnomad AMI
AF:
0.0833
Gnomad AMR
AF:
0.0570
Gnomad ASJ
AF:
0.0381
Gnomad EAS
AF:
0.0113
Gnomad SAS
AF:
0.0128
Gnomad FIN
AF:
0.107
Gnomad MID
AF:
0.0380
Gnomad NFE
AF:
0.0931
Gnomad OTH
AF:
0.0765
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0880
AC:
13405
AN:
152288
Hom.:
607
Cov.:
33
AF XY:
0.0861
AC XY:
6414
AN XY:
74468
show subpopulations
Gnomad4 AFR
AF:
0.110
Gnomad4 AMR
AF:
0.0570
Gnomad4 ASJ
AF:
0.0381
Gnomad4 EAS
AF:
0.0112
Gnomad4 SAS
AF:
0.0130
Gnomad4 FIN
AF:
0.107
Gnomad4 NFE
AF:
0.0931
Gnomad4 OTH
AF:
0.0757
Alfa
AF:
0.0880
Hom.:
290
Bravo
AF:
0.0865
Asia WGS
AF:
0.0260
AC:
90
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
CADD
Benign
0.15
DANN
Benign
0.77

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: rs10484676; hg19: chr6-148304698; API