rs13066103

Variant names:

• chr3-72541749-C-T
• rs13066103
• ENST00000478745.1:n.582+7636G>A

Variant summary

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

The ENST00000478745.1(ENSG00000244345):​n.582+7636G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.594 in 152,084 control chromosomes in the GnomAD database, including 32,712 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 0.59 (32712 hom., cov: 32)
• Consequence: ENSG00000244345 ENST00000478745.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.274
• Publications: 1 publications found

Genes affected

ENSG00000244345 (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 (NFE) allele frequency at 95% confidence interval = 0.79 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000478745.1. 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
	ENSG00000244345	ENST00000478745.1	TSL:3	n.582+7636G>A		intron	N/A
	ENSG00000244345	ENST00000810476.1		n.224+7636G>A		intron	N/A
	ENSG00000244345	ENST00000810477.1		n.193-6982G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.595 AC: 90356 AN: 151966 Hom.: 32695 Cov.: 32

Gnomad AFR AF: 0.159

Gnomad AMI AF: 0.891

Gnomad AMR AF: 0.697

Gnomad ASJ AF: 0.650

Gnomad EAS AF: 0.592

Gnomad SAS AF: 0.686

Gnomad FIN AF: 0.773

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.796

Gnomad OTH AF: 0.604

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

GnomAD4 genome AF: 0.594 AC: 90390 AN: 152084 Hom.: 32712 Cov.: 32 AF XY: 0.596 AC XY: 44307 AN XY: 74318

African (AFR) AF: 0.159 AC: 6586 AN: 41488

American (AMR) AF: 0.698 AC: 10658 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.650 AC: 2255 AN: 3470

East Asian (EAS) AF: 0.592 AC: 3054 AN: 5156

South Asian (SAS) AF: 0.690 AC: 3329 AN: 4824

European-Finnish (FIN) AF: 0.773 AC: 8173 AN: 10574

Middle Eastern (MID) AF: 0.561 AC: 165 AN: 294

European-Non Finnish (NFE) AF: 0.796 AC: 54083 AN: 67984

Other (OTH) AF: 0.606 AC: 1276 AN: 2106

Alfa AF: 0.724 Hom.: 107137

Bravo AF: 0.567

Asia WGS AF: 0.615 AC: 2139 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.0
DANN	Benign	0.69
PhyloP100		-0.27

Splicing

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

Other links and lift over

dbSNP: rs13066103; hg19: chr3-72590900;