rs5017082

Positions:

• chr12-38920762-C-A
• chr12-38920762-C-T

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 0.539 in 151,990 control chromosomes in the GnomAD database, including 25,196 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 0.54 (25196 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.280

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.853 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

Frequencies

GnomAD3 genomes AF: 0.539 AC: 81784 AN: 151872 Hom.: 25129 Cov.: 32

Gnomad AFR AF: 0.860

Gnomad AMI AF: 0.292

Gnomad AMR AF: 0.463

Gnomad ASJ AF: 0.386

Gnomad EAS AF: 0.458

Gnomad SAS AF: 0.369

Gnomad FIN AF: 0.453

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.405

Gnomad OTH AF: 0.478

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

GnomAD4 genome AF: 0.539 AC: 81918 AN: 151990 Hom.: 25196 Cov.: 32 AF XY: 0.535 AC XY: 39755 AN XY: 74278

Gnomad4 AFR AF: 0.860

Gnomad4 AMR AF: 0.463

Gnomad4 ASJ AF: 0.386

Gnomad4 EAS AF: 0.459

Gnomad4 SAS AF: 0.369

Gnomad4 FIN AF: 0.453

Gnomad4 NFE AF: 0.405

Gnomad4 OTH AF: 0.484

Alfa AF: 0.359 Hom.: 1446

Bravo AF: 0.559

Asia WGS AF: 0.454 AC: 1578 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.0
DANN	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5017082; hg19: chr12-39314564;