rs1858163

Variant names:

• chr2-166684677-G-A
• rs1858163

Your query was ambiguous. Multiple possible variants found:

• chr2-166684677-G-A
• chr2-166684677-G-C

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 0.623 in 151,934 control chromosomes in the GnomAD database, including 31,654 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 0.62 (31654 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.335
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.742 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.623 AC: 94655 AN: 151818 Hom.: 31648 Cov.: 31

Gnomad AFR AF: 0.370

Gnomad AMI AF: 0.721

Gnomad AMR AF: 0.724

Gnomad ASJ AF: 0.639

Gnomad EAS AF: 0.569

Gnomad SAS AF: 0.535

Gnomad FIN AF: 0.723

Gnomad MID AF: 0.658

Gnomad NFE AF: 0.747

Gnomad OTH AF: 0.641

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

GnomAD4 genome AF: 0.623 AC: 94678 AN: 151934 Hom.: 31654 Cov.: 31 AF XY: 0.622 AC XY: 46186 AN XY: 74256

African (AFR) AF: 0.369 AC: 15294 AN: 41418

American (AMR) AF: 0.724 AC: 11059 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.639 AC: 2220 AN: 3472

East Asian (EAS) AF: 0.569 AC: 2928 AN: 5150

South Asian (SAS) AF: 0.535 AC: 2569 AN: 4800

European-Finnish (FIN) AF: 0.723 AC: 7631 AN: 10548

Middle Eastern (MID) AF: 0.658 AC: 192 AN: 292

European-Non Finnish (NFE) AF: 0.747 AC: 50785 AN: 67960

Other (OTH) AF: 0.636 AC: 1344 AN: 2112

Alfa AF: 0.670 Hom.: 6195

Bravo AF: 0.616

Asia WGS AF: 0.545 AC: 1894 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.3
DANN	Benign	0.59
PhyloP100		0.34

Splicing

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

Other links and lift over

dbSNP: rs1858163; hg19: chr2-167541187;