rs2842003

Positions:

• chr1-163010505-T-G

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/exons	MANE	UniProt

Ensembl

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