rs9512361

Variant names:

• chr13-26734720-G-A
• rs9512361
• ENST00000849353.1:n.103-5901G>A

Variant summary

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

The ENST00000849353.1(ENSG00000310371):​n.103-5901G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.462 in 152,044 control chromosomes in the GnomAD database, including 16,561 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 0.46 (16561 hom., cov: 33)
• Consequence: ENSG00000310371 ENST00000849353.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.11
• Publications: 1 publications found

Genes affected

ENSG00000310371 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.596 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
ENSG00000310371	ENST00000849353.1	n.103-5901G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.462 AC: 70167 AN: 151926 Hom.: 16549 Cov.: 33

Gnomad AFR AF: 0.357

Gnomad AMI AF: 0.482

Gnomad AMR AF: 0.484

Gnomad ASJ AF: 0.606

Gnomad EAS AF: 0.614

Gnomad SAS AF: 0.500

Gnomad FIN AF: 0.400

Gnomad MID AF: 0.614

Gnomad NFE AF: 0.506

Gnomad OTH AF: 0.497

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

GnomAD4 genome AF: 0.462 AC: 70208 AN: 152044 Hom.: 16561 Cov.: 33 AF XY: 0.459 AC XY: 34091 AN XY: 74318

African (AFR) AF: 0.357 AC: 14809 AN: 41464

American (AMR) AF: 0.485 AC: 7405 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.606 AC: 2100 AN: 3466

East Asian (EAS) AF: 0.614 AC: 3171 AN: 5166

South Asian (SAS) AF: 0.501 AC: 2413 AN: 4820

European-Finnish (FIN) AF: 0.400 AC: 4226 AN: 10564

Middle Eastern (MID) AF: 0.605 AC: 178 AN: 294

European-Non Finnish (NFE) AF: 0.506 AC: 34413 AN: 67974

Other (OTH) AF: 0.500 AC: 1056 AN: 2112

Alfa AF: 0.478 Hom.: 6825

Bravo AF: 0.462

Asia WGS AF: 0.540 AC: 1882 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.14
DANN	Benign	0.63
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs9512361; hg19: chr13-27308857;