1-162034056-G-A

Position:

• chr1-162034056-G-A

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 0.183 in 152,058 control chromosomes in the GnomAD database, including 2,766 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 0.18 (2766 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.05

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.25 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: 0.183 AC: 27782 AN: 151940 Hom.: 2757 Cov.: 33

Gnomad AFR AF: 0.253

Gnomad AMI AF: 0.146

Gnomad AMR AF: 0.132

Gnomad ASJ AF: 0.248

Gnomad EAS AF: 0.182

Gnomad SAS AF: 0.237

Gnomad FIN AF: 0.137

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.151

Gnomad OTH AF: 0.203

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

GnomAD4 genome AF: 0.183 AC: 27827 AN: 152058 Hom.: 2766 Cov.: 33 AF XY: 0.181 AC XY: 13428 AN XY: 74312

Gnomad4 AFR AF: 0.254

Gnomad4 AMR AF: 0.131

Gnomad4 ASJ AF: 0.248

Gnomad4 EAS AF: 0.182

Gnomad4 SAS AF: 0.236

Gnomad4 FIN AF: 0.137

Gnomad4 NFE AF: 0.151

Gnomad4 OTH AF: 0.203

Alfa AF: 0.162 Hom.: 2221

Bravo AF: 0.182

Asia WGS AF: 0.211 AC: 737 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.028
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs885092; hg19: chr1-162003846;