rs10491543

Variant names:

• chr9-82838536-G-A
• rs10491543

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 0.104 in 151,938 control chromosomes in the GnomAD database, including 920 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 0.10 (920 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.442

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.186 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: 0.104 AC: 15840 AN: 151820 Hom.: 918 Cov.: 32

Gnomad AFR AF: 0.118

Gnomad AMI AF: 0.0844

Gnomad AMR AF: 0.121

Gnomad ASJ AF: 0.108

Gnomad EAS AF: 0.0673

Gnomad SAS AF: 0.197

Gnomad FIN AF: 0.0988

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.0889

Gnomad OTH AF: 0.108

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

GnomAD4 genome AF: 0.104 AC: 15868 AN: 151938 Hom.: 920 Cov.: 32 AF XY: 0.107 AC XY: 7957 AN XY: 74258

Gnomad4 AFR AF: 0.119

Gnomad4 AMR AF: 0.121

Gnomad4 ASJ AF: 0.108

Gnomad4 EAS AF: 0.0669

Gnomad4 SAS AF: 0.197

Gnomad4 FIN AF: 0.0988

Gnomad4 NFE AF: 0.0889

Gnomad4 OTH AF: 0.106

Alfa AF: 0.0990 Hom.: 104

Bravo AF: 0.106

Asia WGS AF: 0.138 AC: 479 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	6.6
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10491543; hg19: chr9-85453451;