chr12-52535586-T-C

Variant names:

• chr12-52535586-T-C
• rs585583

Variant summary

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

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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.343

ACMG classification

Verdict is Benign. Variant got -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

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

Gnomad4 AFR AF: 0.120

Gnomad4 AMR AF: 0.489

Gnomad4 ASJ AF: 0.627

Gnomad4 EAS AF: 0.513

Gnomad4 SAS AF: 0.409

Gnomad4 FIN AF: 0.581

Gnomad4 NFE AF: 0.664

Gnomad4 OTH AF: 0.509

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs585583; hg19: chr12-52929370;