12-52535586-T-C

Variant names:

• chr12-52535586-T-C
• rs585583
• ENST00000794060.1:n.551-2582T>C

Variant summary

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

The ENST00000794060.1(ENSG00000303382):​n.551-2582T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.475 in 152,170 control chromosomes in the GnomAD database, including 21,209 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 0.47 (21209 hom., cov: 33)
• Consequence: ENSG00000303382 ENST00000794060.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.343
• Publications: 2 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=-0.71).
• 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.551-2582T>C		intron_variant	Intron 3 of 3
ENSG00000303382	ENST00000794061.1	n.381-2582T>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.475 AC: 72292 AN: 152052 Hom.: 21214 Cov.: 33

Gnomad AFR AF: 0.121

Gnomad AMI AF: 0.512

Gnomad AMR AF: 0.490

Gnomad ASJ AF: 0.627

Gnomad EAS AF: 0.513

Gnomad SAS AF: 0.409

Gnomad FIN AF: 0.581

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.664

Gnomad OTH AF: 0.508

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

GnomAD4 genome AF: 0.475 AC: 72279 AN: 152170 Hom.: 21209 Cov.: 33 AF XY: 0.469 AC XY: 34891 AN XY: 74382

African (AFR) AF: 0.120 AC: 5004 AN: 41562

American (AMR) AF: 0.489 AC: 7468 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.627 AC: 2176 AN: 3470

East Asian (EAS) AF: 0.513 AC: 2653 AN: 5168

South Asian (SAS) AF: 0.409 AC: 1970 AN: 4814

European-Finnish (FIN) AF: 0.581 AC: 6138 AN: 10562

Middle Eastern (MID) AF: 0.527 AC: 155 AN: 294

European-Non Finnish (NFE) AF: 0.664 AC: 45173 AN: 67994

Other (OTH) AF: 0.509 AC: 1075 AN: 2114

Alfa AF: 0.433 Hom.: 1537

Bravo AF: 0.456

Asia WGS AF: 0.378 AC: 1310 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	6.9
DANN	Benign	0.94
PhyloP100		0.34

Splicing

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

Other links and lift over

dbSNP: rs585583; hg19: chr12-52929370;