13-47624581-T-C

Variant names:

• chr13-47624581-T-C
• rs1575891
• ENST00000765501.1:n.79+9678T>C

Variant summary

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

The ENST00000765501.1(ENSG00000299661):​n.79+9678T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.699 in 151,938 control chromosomes in the GnomAD database, including 37,567 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 0.70 (37567 hom., cov: 30)
• Consequence: ENSG00000299661 ENST00000765501.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.168
• Publications: 13 publications found

Genes affected

ENSG00000299661 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.756 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
ENSG00000299661	ENST00000765501.1	n.79+9678T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.699 AC: 106158 AN: 151822 Hom.: 37521 Cov.: 30

Gnomad AFR AF: 0.605

Gnomad AMI AF: 0.769

Gnomad AMR AF: 0.694

Gnomad ASJ AF: 0.697

Gnomad EAS AF: 0.658

Gnomad SAS AF: 0.630

Gnomad FIN AF: 0.717

Gnomad MID AF: 0.753

Gnomad NFE AF: 0.761

Gnomad OTH AF: 0.720

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

GnomAD4 genome AF: 0.699 AC: 106256 AN: 151938 Hom.: 37567 Cov.: 30 AF XY: 0.695 AC XY: 51636 AN XY: 74262

African (AFR) AF: 0.606 AC: 25097 AN: 41426

American (AMR) AF: 0.694 AC: 10587 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.697 AC: 2416 AN: 3466

East Asian (EAS) AF: 0.658 AC: 3385 AN: 5144

South Asian (SAS) AF: 0.631 AC: 3031 AN: 4806

European-Finnish (FIN) AF: 0.717 AC: 7574 AN: 10570

Middle Eastern (MID) AF: 0.752 AC: 221 AN: 294

European-Non Finnish (NFE) AF: 0.761 AC: 51722 AN: 67958

Other (OTH) AF: 0.721 AC: 1525 AN: 2114

Alfa AF: 0.735 Hom.: 109738

Bravo AF: 0.696

Asia WGS AF: 0.661 AC: 2300 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	4.1
DANN	Benign	0.69
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs1575891; hg19: chr13-48198716; COSMIC: COSV69349441;