rs1473307

Variant names:

• chr2-225360907-C-T
• rs1473307

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 0.635 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
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

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: 0.635 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

African (AFR) AF: 0.832 AC: 34529 AN: 41504

American (AMR) AF: 0.608 AC: 9283 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.630 AC: 2186 AN: 3470

East Asian (EAS) AF: 0.373 AC: 1926 AN: 5158

South Asian (SAS) AF: 0.403 AC: 1943 AN: 4816

European-Finnish (FIN) AF: 0.583 AC: 6148 AN: 10548

Middle Eastern (MID) AF: 0.622 AC: 183 AN: 294

European-Non Finnish (NFE) AF: 0.568 AC: 38628 AN: 67966

Other (OTH) AF: 0.620 AC: 1305 AN: 2106

Alfa AF: 0.644 Hom.: 20761

Bravo AF: 0.646

Asia WGS AF: 0.418 AC: 1456 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.6
DANN	Benign	0.76
PhyloP100		-0.77

Splicing

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

Other links and lift over

dbSNP: rs1473307; hg19: chr2-226225623;