rs2225251

Variant names:

• chr1-43063532-C-T
• rs2225251

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 0.467 in 152,104 control chromosomes in the GnomAD database, including 19,896 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 0.47 (19896 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.165
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.624 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: 0.467 AC: 70978 AN: 151986 Hom.: 19897 Cov.: 32

Gnomad AFR AF: 0.143

Gnomad AMI AF: 0.696

Gnomad AMR AF: 0.497

Gnomad ASJ AF: 0.602

Gnomad EAS AF: 0.424

Gnomad SAS AF: 0.520

Gnomad FIN AF: 0.575

Gnomad MID AF: 0.608

Gnomad NFE AF: 0.628

Gnomad OTH AF: 0.500

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

GnomAD4 genome AF: 0.467 AC: 70979 AN: 152104 Hom.: 19896 Cov.: 32 AF XY: 0.466 AC XY: 34625 AN XY: 74320

African (AFR) AF: 0.143 AC: 5933 AN: 41506

American (AMR) AF: 0.496 AC: 7580 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.602 AC: 2091 AN: 3472

East Asian (EAS) AF: 0.424 AC: 2177 AN: 5138

South Asian (SAS) AF: 0.520 AC: 2511 AN: 4826

European-Finnish (FIN) AF: 0.575 AC: 6085 AN: 10580

Middle Eastern (MID) AF: 0.602 AC: 177 AN: 294

European-Non Finnish (NFE) AF: 0.629 AC: 42728 AN: 67984

Other (OTH) AF: 0.503 AC: 1064 AN: 2116

Alfa AF: 0.503 Hom.: 3692

Bravo AF: 0.446

Asia WGS AF: 0.463 AC: 1607 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.6
DANN	Benign	0.66
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs2225251; hg19: chr1-43529203; COSMIC: COSV69714219;