3-122321215-C-T

Variant names:

• chr3-122321215-C-T
• rs9864290

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.624 in 152,028 control chromosomes in the GnomAD database, including 30,465 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 0.62 (30465 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0660
• Publications: 9 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.71 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: 0.624 AC: 94801 AN: 151910 Hom.: 30463 Cov.: 32

Gnomad AFR AF: 0.483

Gnomad AMI AF: 0.816

Gnomad AMR AF: 0.613

Gnomad ASJ AF: 0.638

Gnomad EAS AF: 0.524

Gnomad SAS AF: 0.537

Gnomad FIN AF: 0.674

Gnomad MID AF: 0.614

Gnomad NFE AF: 0.715

Gnomad OTH AF: 0.642

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

GnomAD4 genome AF: 0.624 AC: 94824 AN: 152028 Hom.: 30465 Cov.: 32 AF XY: 0.622 AC XY: 46184 AN XY: 74310

African (AFR) AF: 0.482 AC: 19990 AN: 41444

American (AMR) AF: 0.613 AC: 9369 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.638 AC: 2210 AN: 3464

East Asian (EAS) AF: 0.523 AC: 2702 AN: 5166

South Asian (SAS) AF: 0.535 AC: 2582 AN: 4822

European-Finnish (FIN) AF: 0.674 AC: 7125 AN: 10574

Middle Eastern (MID) AF: 0.602 AC: 177 AN: 294

European-Non Finnish (NFE) AF: 0.715 AC: 48586 AN: 67966

Other (OTH) AF: 0.637 AC: 1342 AN: 2108

Alfa AF: 0.677 Hom.: 96265

Bravo AF: 0.618

Asia WGS AF: 0.484 AC: 1685 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.5
DANN	Benign	0.53
PhyloP100		0.066

Splicing

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

Other links and lift over

dbSNP: rs9864290; hg19: chr3-122040062;