rs13066103

Positions:

• chr3-72541749-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000478745.1(ENSG00000244345):​n.582+7636G>A variant causes a intron, non coding transcript 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: ENST00000478745.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.274

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000478745.1	n.582+7636G>A		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR AF: 0.159

Gnomad4 AMR AF: 0.698

Gnomad4 ASJ AF: 0.650

Gnomad4 EAS AF: 0.592

Gnomad4 SAS AF: 0.690

Gnomad4 FIN AF: 0.773

Gnomad4 NFE AF: 0.796

Gnomad4 OTH AF: 0.606

Alfa AF: 0.756 Hom.: 70811

Bravo AF: 0.567

Asia WGS AF: 0.615 AC: 2139 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13066103; hg19: chr3-72590900;