rs11688834

chr2-174068692-C-T

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.383

Gnomad4 AMR AF: 0.221

Gnomad4 ASJ AF: 0.322

Gnomad4 EAS AF: 0.0274

Gnomad4 SAS AF: 0.198

Gnomad4 FIN AF: 0.199

Gnomad4 NFE AF: 0.272

Gnomad4 OTH AF: 0.306

Alfa AF: 0.277 Hom.: 2798

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11688834; hg19: chr2-174933420;