9-82803131-C-T

Variant names:

• chr9-82803131-C-T
• rs10491547
• ENST00000792604.1:n.354+27907G>A

Variant summary

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

The ENST00000792604.1(ENSG00000303186):​n.354+27907G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.392 in 151,282 control chromosomes in the GnomAD database, including 11,746 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 0.39 (11746 hom., cov: 30)
• Consequence: ENSG00000303186 ENST00000792604.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.106
• 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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.483 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000792604.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000303186	ENST00000792604.1		n.354+27907G>A		intron	N/A
	ENSG00000303186	ENST00000792605.1		n.202-20749G>A		intron	N/A
	ENSG00000303186	ENST00000792606.1		n.163+27907G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.392 AC: 59306 AN: 151166 Hom.: 11747 Cov.: 30

Gnomad AFR AF: 0.344

Gnomad AMI AF: 0.423

Gnomad AMR AF: 0.361

Gnomad ASJ AF: 0.403

Gnomad EAS AF: 0.500

Gnomad SAS AF: 0.361

Gnomad FIN AF: 0.449

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.415

Gnomad OTH AF: 0.351

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

GnomAD4 genome AF: 0.392 AC: 59303 AN: 151282 Hom.: 11746 Cov.: 30 AF XY: 0.392 AC XY: 28962 AN XY: 73830

African (AFR) AF: 0.343 AC: 14160 AN: 41236

American (AMR) AF: 0.360 AC: 5473 AN: 15182

Ashkenazi Jewish (ASJ) AF: 0.403 AC: 1397 AN: 3468

East Asian (EAS) AF: 0.499 AC: 2536 AN: 5078

South Asian (SAS) AF: 0.361 AC: 1726 AN: 4778

European-Finnish (FIN) AF: 0.449 AC: 4661 AN: 10380

Middle Eastern (MID) AF: 0.296 AC: 87 AN: 294

European-Non Finnish (NFE) AF: 0.415 AC: 28151 AN: 67854

Other (OTH) AF: 0.346 AC: 726 AN: 2100

Alfa AF: 0.388 Hom.: 1727

Bravo AF: 0.383

Asia WGS AF: 0.365 AC: 1271 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.80
DANN	Benign	0.68
PhyloP100		0.11

Splicing

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

Other links and lift over

dbSNP: rs10491547; hg19: chr9-85418046;