rs644524

Variant names:

• chr12-52537683-G-A
• rs644524
• ENST00000794060.1:n.551-485G>A

Variant summary

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

The ENST00000794060.1(ENSG00000303382):​n.551-485G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.495 in 152,076 control chromosomes in the GnomAD database, including 20,290 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 0.49 (20290 hom., cov: 32)
• Consequence: ENSG00000303382 ENST00000794060.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0680
• Publications: 4 publications found

Genes affected

ENSG00000303382 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.708 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
ENSG00000303382	ENST00000794060.1	n.551-485G>A		intron_variant	Intron 3 of 3
ENSG00000303382	ENST00000794061.1	n.381-485G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.494 AC: 75106 AN: 151958 Hom.: 20242 Cov.: 32

Gnomad AFR AF: 0.714

Gnomad AMI AF: 0.426

Gnomad AMR AF: 0.444

Gnomad ASJ AF: 0.367

Gnomad EAS AF: 0.126

Gnomad SAS AF: 0.500

Gnomad FIN AF: 0.435

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.416

Gnomad OTH AF: 0.486

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

GnomAD4 genome AF: 0.495 AC: 75212 AN: 152076 Hom.: 20290 Cov.: 32 AF XY: 0.493 AC XY: 36677 AN XY: 74360

African (AFR) AF: 0.715 AC: 29634 AN: 41456

American (AMR) AF: 0.445 AC: 6802 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.367 AC: 1274 AN: 3472

East Asian (EAS) AF: 0.126 AC: 652 AN: 5182

South Asian (SAS) AF: 0.500 AC: 2407 AN: 4812

European-Finnish (FIN) AF: 0.435 AC: 4595 AN: 10574

Middle Eastern (MID) AF: 0.486 AC: 143 AN: 294

European-Non Finnish (NFE) AF: 0.416 AC: 28301 AN: 67974

Other (OTH) AF: 0.481 AC: 1016 AN: 2114

Alfa AF: 0.436 Hom.: 25174

Bravo AF: 0.502

Asia WGS AF: 0.356 AC: 1240 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	6.1
DANN	Benign	0.73
PhyloP100		0.068

Splicing

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

Other links and lift over

dbSNP: rs644524; hg19: chr12-52931467;