13-47629810-T-G

Variant names:

• chr13-47629810-T-G
• rs1853987
• ENST00000765501.1:n.79+14907T>G

Variant summary

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

The ENST00000765501.1(ENSG00000299661):​n.79+14907T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.703 in 151,958 control chromosomes in the GnomAD database, including 37,870 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 (37870 hom., cov: 32)
• Consequence: ENSG00000299661 ENST00000765501.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.39
• Publications: 4 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=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.753 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000765501.1. 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
	ENSG00000299661	ENST00000765501.1		n.79+14907T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.703 AC: 106711 AN: 151840 Hom.: 37822 Cov.: 32

Gnomad AFR AF: 0.622

Gnomad AMI AF: 0.765

Gnomad AMR AF: 0.695

Gnomad ASJ AF: 0.696

Gnomad EAS AF: 0.661

Gnomad SAS AF: 0.629

Gnomad FIN AF: 0.717

Gnomad MID AF: 0.753

Gnomad NFE AF: 0.758

Gnomad OTH AF: 0.725

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

GnomAD4 genome AF: 0.703 AC: 106814 AN: 151958 Hom.: 37870 Cov.: 32 AF XY: 0.699 AC XY: 51909 AN XY: 74262

African (AFR) AF: 0.623 AC: 25791 AN: 41422

American (AMR) AF: 0.695 AC: 10610 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.696 AC: 2415 AN: 3472

East Asian (EAS) AF: 0.661 AC: 3407 AN: 5154

South Asian (SAS) AF: 0.630 AC: 3035 AN: 4816

European-Finnish (FIN) AF: 0.717 AC: 7537 AN: 10518

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

European-Non Finnish (NFE) AF: 0.758 AC: 51567 AN: 67998

Other (OTH) AF: 0.727 AC: 1535 AN: 2112

Alfa AF: 0.693 Hom.: 3819

Bravo AF: 0.701

Asia WGS AF: 0.663 AC: 2303 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	12
DANN	Benign	0.88
PhyloP100		1.4

Splicing

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

Other links and lift over

dbSNP: rs1853987; hg19: chr13-48203945; COSMIC: COSV69349453;