rs1473307

Variant names:

• chr2-225360907-C-T
• rs1473307

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 0.635 in 152,044 control chromosomes in the GnomAD database, including 31,994 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 0.63 (31994 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.766

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.825 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: 0.635 AC: 96450 AN: 151926 Hom.: 31960 Cov.: 32

Gnomad AFR AF: 0.832

Gnomad AMI AF: 0.452

Gnomad AMR AF: 0.608

Gnomad ASJ AF: 0.630

Gnomad EAS AF: 0.374

Gnomad SAS AF: 0.403

Gnomad FIN AF: 0.583

Gnomad MID AF: 0.623

Gnomad NFE AF: 0.568

Gnomad OTH AF: 0.621

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

GnomAD4 genome AF: 0.635 AC: 96542 AN: 152044 Hom.: 31994 Cov.: 32 AF XY: 0.632 AC XY: 46955 AN XY: 74308

Gnomad4 AFR AF: 0.832

Gnomad4 AMR AF: 0.608

Gnomad4 ASJ AF: 0.630

Gnomad4 EAS AF: 0.373

Gnomad4 SAS AF: 0.403

Gnomad4 FIN AF: 0.583

Gnomad4 NFE AF: 0.568

Gnomad4 OTH AF: 0.620

Alfa AF: 0.617 Hom.: 6695

Bravo AF: 0.646

Asia WGS AF: 0.418 AC: 1456 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.6
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1473307; hg19: chr2-226225623;