rs10491543

Variant names:

• chr9-82838536-G-A
• rs10491543
• ENST00000792604.1:n.266-7410C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000792604.1(ENSG00000303186):​n.266-7410C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. 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: ENSG00000303186 ENST00000792604.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.442
• Publications: 1 publications found

Genes affected

ENSG00000303186 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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
ENSG00000303186	ENST00000792604.1	n.266-7410C>T		intron_variant	Intron 3 of 4
ENSG00000303186	ENST00000792605.1	n.113-7410C>T		intron_variant	Intron 1 of 3
ENSG00000303186	ENST00000792606.1	n.75-7410C>T		intron_variant	Intron 1 of 2

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

African (AFR) AF: 0.119 AC: 4919 AN: 41460

American (AMR) AF: 0.121 AC: 1848 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.108 AC: 374 AN: 3468

East Asian (EAS) AF: 0.0669 AC: 345 AN: 5156

South Asian (SAS) AF: 0.197 AC: 946 AN: 4806

European-Finnish (FIN) AF: 0.0988 AC: 1044 AN: 10570

Middle Eastern (MID) AF: 0.170 AC: 50 AN: 294

European-Non Finnish (NFE) AF: 0.0889 AC: 6040 AN: 67922

Other (OTH) AF: 0.106 AC: 225 AN: 2114

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
PhyloP100		0.44

Splicing

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

Other links and lift over

dbSNP: rs10491543; hg19: chr9-85453451;