rs11688834

Variant names:

• chr2-174068692-C-T
• rs11688834

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.284 in 152,008 control chromosomes in the GnomAD database, including 6,611 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 0.28 (6611 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.887
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.36).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.378 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: 0.284 AC: 43090 AN: 151890 Hom.: 6595 Cov.: 32

Gnomad AFR AF: 0.383

Gnomad AMI AF: 0.331

Gnomad AMR AF: 0.221

Gnomad ASJ AF: 0.322

Gnomad EAS AF: 0.0275

Gnomad SAS AF: 0.196

Gnomad FIN AF: 0.199

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.272

Gnomad OTH AF: 0.306

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

GnomAD4 genome AF: 0.284 AC: 43147 AN: 152008 Hom.: 6611 Cov.: 32 AF XY: 0.278 AC XY: 20666 AN XY: 74322

African (AFR) AF: 0.383 AC: 15881 AN: 41440

American (AMR) AF: 0.221 AC: 3372 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.322 AC: 1119 AN: 3470

East Asian (EAS) AF: 0.0274 AC: 142 AN: 5190

South Asian (SAS) AF: 0.198 AC: 953 AN: 4822

European-Finnish (FIN) AF: 0.199 AC: 2101 AN: 10542

Middle Eastern (MID) AF: 0.395 AC: 116 AN: 294

European-Non Finnish (NFE) AF: 0.272 AC: 18514 AN: 67950

Other (OTH) AF: 0.306 AC: 647 AN: 2114

Alfa AF: 0.278 Hom.: 3139

Bravo AF: 0.290

Asia WGS AF: 0.146 AC: 509 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.36
CADD	Benign	16
DANN	Benign	0.58
PhyloP100		0.89

Splicing

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

Other links and lift over

dbSNP: rs11688834; hg19: chr2-174933420;