rs9838682

Variant names:

• chr3-30349375-A-G
• rs9838682
• ENST00000813769.1:n.506-8052T>C

Variant summary

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

The ENST00000813769.1(ENSG00000227549):​n.506-8052T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.569 in 151,834 control chromosomes in the GnomAD database, including 25,553 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 0.57 (25553 hom., cov: 31)
• Consequence: ENSG00000227549 ENST00000813769.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.732
• Publications: 13 publications found

Genes affected

ENSG00000227549 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.637 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
ENSG00000227549	ENST00000813769.1	n.506-8052T>C		intron_variant	Intron 5 of 5

Frequencies

GnomAD3 genomes AF: 0.569 AC: 86363 AN: 151716 Hom.: 25542 Cov.: 31

Gnomad AFR AF: 0.397

Gnomad AMI AF: 0.698

Gnomad AMR AF: 0.643

Gnomad ASJ AF: 0.535

Gnomad EAS AF: 0.623

Gnomad SAS AF: 0.656

Gnomad FIN AF: 0.662

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.633

Gnomad OTH AF: 0.559

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

GnomAD4 genome AF: 0.569 AC: 86414 AN: 151834 Hom.: 25553 Cov.: 31 AF XY: 0.572 AC XY: 42455 AN XY: 74186

African (AFR) AF: 0.397 AC: 16432 AN: 41394

American (AMR) AF: 0.643 AC: 9818 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.535 AC: 1855 AN: 3466

East Asian (EAS) AF: 0.623 AC: 3191 AN: 5120

South Asian (SAS) AF: 0.656 AC: 3155 AN: 4812

European-Finnish (FIN) AF: 0.662 AC: 6991 AN: 10564

Middle Eastern (MID) AF: 0.476 AC: 140 AN: 294

European-Non Finnish (NFE) AF: 0.633 AC: 43018 AN: 67908

Other (OTH) AF: 0.561 AC: 1182 AN: 2108

Alfa AF: 0.612 Hom.: 45915

Bravo AF: 0.556

Asia WGS AF: 0.614 AC: 2137 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	4.7
DANN	Benign	0.42
PhyloP100		0.73

Splicing

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

Other links and lift over

dbSNP: rs9838682; hg19: chr3-30390867;