13-104966064-G-T

Variant names:

• chr13-104966064-G-T
• rs9332445
• ENST00000731281.1:n.61+2876C>A

Variant summary

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

The ENST00000731281.1(ENSG00000295604):​n.61+2876C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.338 in 151,392 control chromosomes in the GnomAD database, including 9,325 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 0.34 (9325 hom., cov: 32)
• Consequence: ENSG00000295604 ENST00000731281.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.89
• Publications: 3 publications found

Genes affected

ENSG00000295604 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.461 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000731281.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000295604	ENST00000731281.1		n.61+2876C>A		intron	N/A
	ENSG00000295604	ENST00000731282.1		n.70+2876C>A		intron	N/A
	ENSG00000295604	ENST00000731283.1		n.69+2876C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.338 AC: 51108 AN: 151276 Hom.: 9325 Cov.: 32

Gnomad AFR AF: 0.187

Gnomad AMI AF: 0.414

Gnomad AMR AF: 0.365

Gnomad ASJ AF: 0.397

Gnomad EAS AF: 0.476

Gnomad SAS AF: 0.463

Gnomad FIN AF: 0.387

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.392

Gnomad OTH AF: 0.350

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

GnomAD4 genome AF: 0.338 AC: 51117 AN: 151392 Hom.: 9325 Cov.: 32 AF XY: 0.341 AC XY: 25190 AN XY: 73968

African (AFR) AF: 0.187 AC: 7709 AN: 41298

American (AMR) AF: 0.365 AC: 5559 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.397 AC: 1374 AN: 3462

East Asian (EAS) AF: 0.477 AC: 2447 AN: 5134

South Asian (SAS) AF: 0.464 AC: 2231 AN: 4812

European-Finnish (FIN) AF: 0.387 AC: 4034 AN: 10418

Middle Eastern (MID) AF: 0.357 AC: 105 AN: 294

European-Non Finnish (NFE) AF: 0.392 AC: 26548 AN: 67730

Other (OTH) AF: 0.348 AC: 732 AN: 2106

Alfa AF: 0.373 Hom.: 5600

Bravo AF: 0.330

Asia WGS AF: 0.428 AC: 1481 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.0050
DANN	Benign	0.31
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs9332445; hg19: chr13-105618415;