rs585224

Variant names:

• chr12-52529088-A-G
• rs585224
• ENST00000794060.1:n.551-9080A>G

Variant summary

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

The ENST00000794060.1(ENSG00000303382):​n.551-9080A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.504 in 152,076 control chromosomes in the GnomAD database, including 21,939 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 0.50 (21939 hom., cov: 32)
• Consequence: ENSG00000303382 ENST00000794060.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.90
• Publications: 6 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=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.659 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.551-9080A>G		intron_variant	Intron 3 of 3
ENSG00000303382	ENST00000794061.1	n.381-9080A>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.504 AC: 76658 AN: 151958 Hom.: 21943 Cov.: 32

Gnomad AFR AF: 0.225

Gnomad AMI AF: 0.514

Gnomad AMR AF: 0.500

Gnomad ASJ AF: 0.626

Gnomad EAS AF: 0.506

Gnomad SAS AF: 0.403

Gnomad FIN AF: 0.578

Gnomad MID AF: 0.528

Gnomad NFE AF: 0.664

Gnomad OTH AF: 0.532

GnomAD2 exomes AF: 0.655 AC: 38 AN: 58 AF XY: 0.800

Gnomad AFR exome AF: 0.583

Gnomad ASJ exome AF: 0.500

Gnomad FIN exome AF: 0.750

Gnomad NFE exome AF: 0.667

Gnomad OTH exome AF: 1.00

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

GnomAD4 genome AF: 0.504 AC: 76662 AN: 152076 Hom.: 21939 Cov.: 32 AF XY: 0.497 AC XY: 36899 AN XY: 74314

African (AFR) AF: 0.224 AC: 9298 AN: 41478

American (AMR) AF: 0.499 AC: 7628 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.626 AC: 2175 AN: 3472

East Asian (EAS) AF: 0.506 AC: 2608 AN: 5150

South Asian (SAS) AF: 0.403 AC: 1943 AN: 4822

European-Finnish (FIN) AF: 0.578 AC: 6114 AN: 10578

Middle Eastern (MID) AF: 0.531 AC: 156 AN: 294

European-Non Finnish (NFE) AF: 0.664 AC: 45149 AN: 67972

Other (OTH) AF: 0.532 AC: 1123 AN: 2112

Alfa AF: 0.617 Hom.: 50543

Bravo AF: 0.489

Asia WGS AF: 0.379 AC: 1315 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	14
DANN	Benign	0.49
PhyloP100		1.9

Splicing

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

Other links and lift over

dbSNP: rs585224; hg19: chr12-52922872;