rs2873551

chr1-54752234-T-C

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;