rs2920500

Positions:

• chr3-12281914-G-A
• chr3-12281914-G-C

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 0.499 in 151,782 control chromosomes in the GnomAD database, including 20,618 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 (20618 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.979

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.902 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.499 AC: 75754 AN: 151664 Hom.: 20614 Cov.: 30

Gnomad AFR AF: 0.323

Gnomad AMI AF: 0.417

Gnomad AMR AF: 0.621

Gnomad ASJ AF: 0.372

Gnomad EAS AF: 0.924

Gnomad SAS AF: 0.779

Gnomad FIN AF: 0.570

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.525

Gnomad OTH AF: 0.475

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

GnomAD4 genome AF: 0.499 AC: 75782 AN: 151782 Hom.: 20618 Cov.: 30 AF XY: 0.509 AC XY: 37725 AN XY: 74144

Gnomad4 AFR AF: 0.323

Gnomad4 AMR AF: 0.621

Gnomad4 ASJ AF: 0.372

Gnomad4 EAS AF: 0.924

Gnomad4 SAS AF: 0.779

Gnomad4 FIN AF: 0.570

Gnomad4 NFE AF: 0.525

Gnomad4 OTH AF: 0.477

Alfa AF: 0.520 Hom.: 27222

Bravo AF: 0.489

Asia WGS AF: 0.798 AC: 2776 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.12
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2920500; hg19: chr3-12323413;