rs2821557

Positions:

• chr1-110676298-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 0.601 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;