rs2821557

Variant names:

• chr1-110676298-C-T
• rs2821557

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 0.601 in 152,048 control chromosomes in the GnomAD database, including 27,878 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 0.60 (27878 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0820

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.708 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: 0.601 AC: 91255 AN: 151930 Hom.: 27843 Cov.: 32

Gnomad AFR AF: 0.714

Gnomad AMI AF: 0.491

Gnomad AMR AF: 0.592

Gnomad ASJ AF: 0.655

Gnomad EAS AF: 0.423

Gnomad SAS AF: 0.438

Gnomad FIN AF: 0.577

Gnomad MID AF: 0.677

Gnomad NFE AF: 0.559

Gnomad OTH AF: 0.635

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

GnomAD4 genome AF: 0.601 AC: 91347 AN: 152048 Hom.: 27878 Cov.: 32 AF XY: 0.598 AC XY: 44466 AN XY: 74308

Gnomad4 AFR AF: 0.714

Gnomad4 AMR AF: 0.592

Gnomad4 ASJ AF: 0.655

Gnomad4 EAS AF: 0.423

Gnomad4 SAS AF: 0.440

Gnomad4 FIN AF: 0.577

Gnomad4 NFE AF: 0.559

Gnomad4 OTH AF: 0.635

Alfa AF: 0.581 Hom.: 43247

Bravo AF: 0.610

Asia WGS AF: 0.491 AC: 1708 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.7
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2821557; hg19: chr1-111218920;