rs2063142

chr1-163083499-A-Gchr1-163083499-A-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 0.196 in 152,036 control chromosomes in the GnomAD database, including 3,424 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 0.20 (3424 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.581

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 (EAS) allele frequency at 95% confidence interval = 0.339 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: 0.196 AC: 29813 AN: 151918 Hom.: 3424 Cov.: 31

Gnomad AFR AF: 0.0935

Gnomad AMI AF: 0.281

Gnomad AMR AF: 0.154

Gnomad ASJ AF: 0.230

Gnomad EAS AF: 0.352

Gnomad SAS AF: 0.214

Gnomad FIN AF: 0.200

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.252

Gnomad OTH AF: 0.192

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

GnomAD4 genome AF: 0.196 AC: 29806 AN: 152036 Hom.: 3424 Cov.: 31 AF XY: 0.193 AC XY: 14371 AN XY: 74318

Gnomad4 AFR AF: 0.0933

Gnomad4 AMR AF: 0.154

Gnomad4 ASJ AF: 0.230

Gnomad4 EAS AF: 0.352

Gnomad4 SAS AF: 0.214

Gnomad4 FIN AF: 0.200

Gnomad4 NFE AF: 0.252

Gnomad4 OTH AF: 0.190

Alfa AF: 0.238 Hom.: 7493

Bravo AF: 0.193

Asia WGS AF: 0.244 AC: 847 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	1.2
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: rs2063142; hg19: chr1-163053289;