rs3922762

Positions:

• chr12-84745301-A-G

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;