chr1-162034056-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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;