rs2225251

Positions:

• chr1-43063532-C-T

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 0.467 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.143

Gnomad4 AMR AF: 0.496

Gnomad4 ASJ AF: 0.602

Gnomad4 EAS AF: 0.424

Gnomad4 SAS AF: 0.520

Gnomad4 FIN AF: 0.575

Gnomad4 NFE AF: 0.629

Gnomad4 OTH AF: 0.503

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

Splicing

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

Publications

LitVar

Other links and lift over

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