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. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.483 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

Gnomad4 AFR AF: 0.207

Gnomad4 AMR AF: 0.440

Gnomad4 ASJ AF: 0.627

Gnomad4 EAS AF: 0.176

Gnomad4 SAS AF: 0.504

Gnomad4 FIN AF: 0.634

Gnomad4 NFE AF: 0.649

Gnomad4 OTH AF: 0.517

Alfa AF: 0.618 Hom.: 46914

Bravo AF: 0.458

Asia WGS AF: 0.330 AC: 1154 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1686103; hg19: chr2-36354621;