chr1-163083499-A-G

Variant names:

• chr1-163083499-A-G
• rs2063142

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.0933 AC: 3866 AN: 41454

American (AMR) AF: 0.154 AC: 2347 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.230 AC: 797 AN: 3470

East Asian (EAS) AF: 0.352 AC: 1814 AN: 5152

South Asian (SAS) AF: 0.214 AC: 1029 AN: 4814

European-Finnish (FIN) AF: 0.200 AC: 2110 AN: 10566

Middle Eastern (MID) AF: 0.265 AC: 78 AN: 294

European-Non Finnish (NFE) AF: 0.252 AC: 17110 AN: 67990

Other (OTH) AF: 0.190 AC: 400 AN: 2108

Alfa AF: 0.228 Hom.: 11812

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
PhyloP100		-0.58

Splicing

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

Other links and lift over

dbSNP: rs2063142; hg19: chr1-163053289;