rs2842003

Variant names:

• chr1-163010505-T-G
• rs2842003

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 0.539 in 151,970 control chromosomes in the GnomAD database, including 22,886 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 0.54 (22886 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.276

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.7 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: 0.540 AC: 81929 AN: 151852 Hom.: 22877 Cov.: 32

Gnomad AFR AF: 0.402

Gnomad AMI AF: 0.639

Gnomad AMR AF: 0.607

Gnomad ASJ AF: 0.563

Gnomad EAS AF: 0.716

Gnomad SAS AF: 0.720

Gnomad FIN AF: 0.558

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.577

Gnomad OTH AF: 0.525

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

GnomAD4 genome AF: 0.539 AC: 81961 AN: 151970 Hom.: 22886 Cov.: 32 AF XY: 0.545 AC XY: 40434 AN XY: 74256

Gnomad4 AFR AF: 0.401

Gnomad4 AMR AF: 0.608

Gnomad4 ASJ AF: 0.563

Gnomad4 EAS AF: 0.716

Gnomad4 SAS AF: 0.720

Gnomad4 FIN AF: 0.558

Gnomad4 NFE AF: 0.577

Gnomad4 OTH AF: 0.523

Alfa AF: 0.560 Hom.: 22390

Bravo AF: 0.536

Asia WGS AF: 0.680 AC: 2365 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.9
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2842003; hg19: chr1-162980295;