rs1686103

chr2-36127478-A-Cchr2-36127478-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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;