rs601225

chr3-101861806-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 0.552 in 151,842 control chromosomes in the GnomAD database, including 24,272 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 0.55 (24272 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.442

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.656 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: 0.552 AC: 83753 AN: 151724 Hom.: 24256 Cov.: 32

Gnomad AFR AF: 0.373

Gnomad AMI AF: 0.601

Gnomad AMR AF: 0.667

Gnomad ASJ AF: 0.603

Gnomad EAS AF: 0.462

Gnomad SAS AF: 0.497

Gnomad FIN AF: 0.541

Gnomad MID AF: 0.528

Gnomad NFE AF: 0.643

Gnomad OTH AF: 0.567

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

GnomAD4 genome AF: 0.552 AC: 83817 AN: 151842 Hom.: 24272 Cov.: 32 AF XY: 0.546 AC XY: 40548 AN XY: 74196

Gnomad4 AFR AF: 0.373

Gnomad4 AMR AF: 0.667

Gnomad4 ASJ AF: 0.603

Gnomad4 EAS AF: 0.461

Gnomad4 SAS AF: 0.499

Gnomad4 FIN AF: 0.541

Gnomad4 NFE AF: 0.643

Gnomad4 OTH AF: 0.571

Alfa AF: 0.613 Hom.: 14627

Bravo AF: 0.561

Asia WGS AF: 0.461 AC: 1603 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	5.2
Dann	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs601225; hg19: chr3-101580650;