rs11685480

Variant names:

• chr2-102310626-G-A
• rs11685480

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 0.479 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
• Publications: 15 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.420 AC: 17380 AN: 41394

American (AMR) AF: 0.403 AC: 6139 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.522 AC: 1810 AN: 3470

East Asian (EAS) AF: 0.531 AC: 2734 AN: 5152

South Asian (SAS) AF: 0.439 AC: 2109 AN: 4808

European-Finnish (FIN) AF: 0.489 AC: 5136 AN: 10506

Middle Eastern (MID) AF: 0.633 AC: 186 AN: 294

European-Non Finnish (NFE) AF: 0.525 AC: 35680 AN: 67944

Other (OTH) AF: 0.516 AC: 1089 AN: 2112

Alfa AF: 0.496 Hom.: 3292

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
PhyloP100		-1.0

Splicing

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

Other links and lift over

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