rs3922762

Variant names:

• chr12-84745301-A-G
• rs3922762

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 0.629 in 152,078 control chromosomes in the GnomAD database, including 31,510 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 0.63 (31510 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.952

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 (AMR) allele frequency at 95% confidence interval = 0.753 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: 0.630 AC: 95686 AN: 151960 Hom.: 31505 Cov.: 33

Gnomad AFR AF: 0.428

Gnomad AMI AF: 0.740

Gnomad AMR AF: 0.765

Gnomad ASJ AF: 0.770

Gnomad EAS AF: 0.642

Gnomad SAS AF: 0.638

Gnomad FIN AF: 0.740

Gnomad MID AF: 0.750

Gnomad NFE AF: 0.693

Gnomad OTH AF: 0.678

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

GnomAD4 genome AF: 0.629 AC: 95717 AN: 152078 Hom.: 31510 Cov.: 33 AF XY: 0.635 AC XY: 47204 AN XY: 74334

Gnomad4 AFR AF: 0.427

Gnomad4 AMR AF: 0.765

Gnomad4 ASJ AF: 0.770

Gnomad4 EAS AF: 0.642

Gnomad4 SAS AF: 0.637

Gnomad4 FIN AF: 0.740

Gnomad4 NFE AF: 0.693

Gnomad4 OTH AF: 0.680

Alfa AF: 0.693 Hom.: 61694

Bravo AF: 0.625

Asia WGS AF: 0.645 AC: 2242 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	0.34
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3922762; hg19: chr12-85139080;