rs2873551

Variant names:

• chr1-54752234-T-C
• rs2873551

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 0.364 in 152,080 control chromosomes in the GnomAD database, including 10,351 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 0.36 (10351 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.447

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.548 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: 0.364 AC: 55281 AN: 151962 Hom.: 10339 Cov.: 33

Gnomad AFR AF: 0.305

Gnomad AMI AF: 0.576

Gnomad AMR AF: 0.434

Gnomad ASJ AF: 0.422

Gnomad EAS AF: 0.565

Gnomad SAS AF: 0.257

Gnomad FIN AF: 0.348

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.373

Gnomad OTH AF: 0.354

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

GnomAD4 genome AF: 0.364 AC: 55318 AN: 152080 Hom.: 10351 Cov.: 33 AF XY: 0.362 AC XY: 26913 AN XY: 74304

Gnomad4 AFR AF: 0.305

Gnomad4 AMR AF: 0.434

Gnomad4 ASJ AF: 0.422

Gnomad4 EAS AF: 0.565

Gnomad4 SAS AF: 0.256

Gnomad4 FIN AF: 0.348

Gnomad4 NFE AF: 0.373

Gnomad4 OTH AF: 0.355

Alfa AF: 0.368 Hom.: 9915

Bravo AF: 0.378

Asia WGS AF: 0.404 AC: 1404 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.9
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2873551; hg19: chr1-55217907;