rs11687765

Positions:

• chr2-82098407-C-A

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 0.463 in 151,914 control chromosomes in the GnomAD database, including 16,434 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 0.46 (16434 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0930

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.568 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.463 AC: 70274 AN: 151798 Hom.: 16422 Cov.: 33

Gnomad AFR AF: 0.406

Gnomad AMI AF: 0.398

Gnomad AMR AF: 0.544

Gnomad ASJ AF: 0.397

Gnomad EAS AF: 0.586

Gnomad SAS AF: 0.448

Gnomad FIN AF: 0.488

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.471

Gnomad OTH AF: 0.459

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

GnomAD4 genome AF: 0.463 AC: 70307 AN: 151914 Hom.: 16434 Cov.: 33 AF XY: 0.466 AC XY: 34573 AN XY: 74214

Gnomad4 AFR AF: 0.406

Gnomad4 AMR AF: 0.544

Gnomad4 ASJ AF: 0.397

Gnomad4 EAS AF: 0.586

Gnomad4 SAS AF: 0.449

Gnomad4 FIN AF: 0.488

Gnomad4 NFE AF: 0.471

Gnomad4 OTH AF: 0.462

Alfa AF: 0.471 Hom.: 20820

Bravo AF: 0.465

Asia WGS AF: 0.550 AC: 1914 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.98
DANN	Benign	0.20

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11687765; hg19: chr2-82325531;