rs11687765

Variant names:

• chr2-82098407-C-A
• rs11687765

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 0.463 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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.406 AC: 16804 AN: 41416

American (AMR) AF: 0.544 AC: 8308 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.397 AC: 1380 AN: 3472

East Asian (EAS) AF: 0.586 AC: 3015 AN: 5148

South Asian (SAS) AF: 0.449 AC: 2161 AN: 4814

European-Finnish (FIN) AF: 0.488 AC: 5140 AN: 10526

Middle Eastern (MID) AF: 0.466 AC: 137 AN: 294

European-Non Finnish (NFE) AF: 0.471 AC: 32024 AN: 67960

Other (OTH) AF: 0.462 AC: 976 AN: 2114

Alfa AF: 0.467 Hom.: 28211

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
PhyloP100		-0.093

Splicing

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

Other links and lift over

dbSNP: rs11687765; hg19: chr2-82325531;