3-122303570-G-C

Variant names:

• chr3-122303570-G-C
• rs1402200

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 0.642 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.643 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

Gnomad4 AFR AF: 0.570

Gnomad4 AMR AF: 0.622

Gnomad4 ASJ AF: 0.663

Gnomad4 EAS AF: 0.515

Gnomad4 SAS AF: 0.541

Gnomad4 FIN AF: 0.664

Gnomad4 NFE AF: 0.702

Gnomad4 OTH AF: 0.655

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1402200; hg19: chr3-122022417;