rs1686103

Variant names:

• chr2-36127478-A-C
• rs1686103

Your query was ambiguous. Multiple possible variants found:

• chr2-36127478-A-C
• chr2-36127478-A-G

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 0.483 in 151,112 control chromosomes in the GnomAD database, including 20,704 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 0.48 (20704 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.04
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.644 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.483 AC: 72927 AN: 150998 Hom.: 20705 Cov.: 29

Gnomad AFR AF: 0.207

Gnomad AMI AF: 0.588

Gnomad AMR AF: 0.441

Gnomad ASJ AF: 0.627

Gnomad EAS AF: 0.175

Gnomad SAS AF: 0.501

Gnomad FIN AF: 0.634

Gnomad MID AF: 0.544

Gnomad NFE AF: 0.649

Gnomad OTH AF: 0.521

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

GnomAD4 genome AF: 0.483 AC: 72922 AN: 151112 Hom.: 20704 Cov.: 29 AF XY: 0.477 AC XY: 35203 AN XY: 73764

African (AFR) AF: 0.207 AC: 8535 AN: 41296

American (AMR) AF: 0.440 AC: 6689 AN: 15206

Ashkenazi Jewish (ASJ) AF: 0.627 AC: 2173 AN: 3464

East Asian (EAS) AF: 0.176 AC: 905 AN: 5150

South Asian (SAS) AF: 0.504 AC: 2409 AN: 4784

European-Finnish (FIN) AF: 0.634 AC: 6474 AN: 10214

Middle Eastern (MID) AF: 0.531 AC: 156 AN: 294

European-Non Finnish (NFE) AF: 0.649 AC: 43966 AN: 67704

Other (OTH) AF: 0.517 AC: 1083 AN: 2096

Alfa AF: 0.601 Hom.: 66532

Bravo AF: 0.458

Asia WGS AF: 0.330 AC: 1154 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	6.5
DANN	Benign	0.53
PhyloP100		1.0

Splicing

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

Other links and lift over

dbSNP: rs1686103; hg19: chr2-36354621;