rs885092

Variant names:

• chr1-162034056-G-A
• rs885092

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 0.183 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
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.254 AC: 10513 AN: 41428

American (AMR) AF: 0.131 AC: 2008 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.248 AC: 861 AN: 3466

East Asian (EAS) AF: 0.182 AC: 942 AN: 5184

South Asian (SAS) AF: 0.236 AC: 1137 AN: 4808

European-Finnish (FIN) AF: 0.137 AC: 1443 AN: 10550

Middle Eastern (MID) AF: 0.286 AC: 84 AN: 294

European-Non Finnish (NFE) AF: 0.151 AC: 10277 AN: 68010

Other (OTH) AF: 0.203 AC: 429 AN: 2112

Alfa AF: 0.165 Hom.: 2963

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
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs885092; hg19: chr1-162003846;