rs11592457

chr10-83396018-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.0658 in 149,868 control chromosomes in the GnomAD database, including 372 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 0.066 (372 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.548

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0933 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: 0.0657 AC: 9843 AN: 149750 Hom.: 367 Cov.: 31

Gnomad AFR AF: 0.0959

Gnomad AMI AF: 0.0747

Gnomad AMR AF: 0.0604

Gnomad ASJ AF: 0.0394

Gnomad EAS AF: 0.0476

Gnomad SAS AF: 0.0255

Gnomad FIN AF: 0.0870

Gnomad MID AF: 0.0510

Gnomad NFE AF: 0.0515

Gnomad OTH AF: 0.0484

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0658 AC: 9858 AN: 149868 Hom.: 372 Cov.: 31 AF XY: 0.0652 AC XY: 4767 AN XY: 73070

Gnomad4 AFR AF: 0.0958

Gnomad4 AMR AF: 0.0610

Gnomad4 ASJ AF: 0.0394

Gnomad4 EAS AF: 0.0473

Gnomad4 SAS AF: 0.0253

Gnomad4 FIN AF: 0.0870

Gnomad4 NFE AF: 0.0515

Gnomad4 OTH AF: 0.0484

Alfa AF: 0.0611 Hom.: 71

Bravo AF: 0.0651

Asia WGS AF: 0.0370 AC: 127 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	4.6
Dann	Benign	0.60

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs11592457; hg19: chr10-85155774;