3-122303570-G-C

Variant names:

• chr3-122303570-G-C
• rs1402200

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 0.642 in 151,786 control chromosomes in the GnomAD database, including 31,718 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 0.64 (31718 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.528
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.696 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.643 AC: 97487 AN: 151668 Hom.: 31716 Cov.: 32

Gnomad AFR AF: 0.570

Gnomad AMI AF: 0.799

Gnomad AMR AF: 0.622

Gnomad ASJ AF: 0.663

Gnomad EAS AF: 0.516

Gnomad SAS AF: 0.542

Gnomad FIN AF: 0.664

Gnomad MID AF: 0.627

Gnomad NFE AF: 0.702

Gnomad OTH AF: 0.660

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

GnomAD4 genome AF: 0.642 AC: 97520 AN: 151786 Hom.: 31718 Cov.: 32 AF XY: 0.639 AC XY: 47398 AN XY: 74162

African (AFR) AF: 0.570 AC: 23566 AN: 41370

American (AMR) AF: 0.622 AC: 9493 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.663 AC: 2295 AN: 3464

East Asian (EAS) AF: 0.515 AC: 2662 AN: 5164

South Asian (SAS) AF: 0.541 AC: 2600 AN: 4808

European-Finnish (FIN) AF: 0.664 AC: 6959 AN: 10480

Middle Eastern (MID) AF: 0.616 AC: 181 AN: 294

European-Non Finnish (NFE) AF: 0.702 AC: 47654 AN: 67926

Other (OTH) AF: 0.655 AC: 1381 AN: 2108

Alfa AF: 0.554 Hom.: 1581

Bravo AF: 0.640

Asia WGS AF: 0.481 AC: 1665 AN: 3456

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	4.1
DANN	Benign	0.73
PhyloP100		0.53

Splicing

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

Other links and lift over

dbSNP: rs1402200; hg19: chr3-122022417;