chr3-122321763-C-T

Variant names:

• chr3-122321763-C-T
• rs6803098

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 152,056 control chromosomes in the GnomAD database, including 30,482 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 (30482 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.615
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.71 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.624 AC: 94857 AN: 151938 Hom.: 30480 Cov.: 32

Gnomad AFR AF: 0.483

Gnomad AMI AF: 0.815

Gnomad AMR AF: 0.613

Gnomad ASJ AF: 0.638

Gnomad EAS AF: 0.524

Gnomad SAS AF: 0.537

Gnomad FIN AF: 0.675

Gnomad MID AF: 0.614

Gnomad NFE AF: 0.715

Gnomad OTH AF: 0.641

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

GnomAD4 genome AF: 0.624 AC: 94880 AN: 152056 Hom.: 30482 Cov.: 32 AF XY: 0.622 AC XY: 46219 AN XY: 74342

African (AFR) AF: 0.483 AC: 19995 AN: 41428

American (AMR) AF: 0.613 AC: 9371 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.638 AC: 2213 AN: 3470

East Asian (EAS) AF: 0.524 AC: 2707 AN: 5168

South Asian (SAS) AF: 0.536 AC: 2582 AN: 4816

European-Finnish (FIN) AF: 0.675 AC: 7145 AN: 10582

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

European-Non Finnish (NFE) AF: 0.715 AC: 48605 AN: 67988

Other (OTH) AF: 0.635 AC: 1343 AN: 2114

Alfa AF: 0.588 Hom.: 3386

Bravo AF: 0.618

Asia WGS AF: 0.484 AC: 1685 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.9
DANN	Benign	0.72
PhyloP100		-0.61

Splicing

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

Other links and lift over

dbSNP: rs6803098; hg19: chr3-122040610;