rs11685480

Variant names:

• chr2-102310626-G-A
• rs11685480

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 0.479 in 151,822 control chromosomes in the GnomAD database, including 17,666 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 (17666 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.521 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: 0.479 AC: 72604 AN: 151704 Hom.: 17647 Cov.: 30

Gnomad AFR AF: 0.420

Gnomad AMI AF: 0.432

Gnomad AMR AF: 0.404

Gnomad ASJ AF: 0.522

Gnomad EAS AF: 0.530

Gnomad SAS AF: 0.437

Gnomad FIN AF: 0.489

Gnomad MID AF: 0.627

Gnomad NFE AF: 0.525

Gnomad OTH AF: 0.509

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

GnomAD4 genome AF: 0.479 AC: 72654 AN: 151822 Hom.: 17666 Cov.: 30 AF XY: 0.475 AC XY: 35257 AN XY: 74188

Gnomad4 AFR AF: 0.420

Gnomad4 AMR AF: 0.403

Gnomad4 ASJ AF: 0.522

Gnomad4 EAS AF: 0.531

Gnomad4 SAS AF: 0.439

Gnomad4 FIN AF: 0.489

Gnomad4 NFE AF: 0.525

Gnomad4 OTH AF: 0.516

Alfa AF: 0.504 Hom.: 2799

Bravo AF: 0.466

Asia WGS AF: 0.503 AC: 1751 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.69
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11685480; hg19: chr2-102927086; COSMIC: COSV52113548;