rs11688246

chr2-85478554-C-Achr2-85478554-C-T

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 0.0381 in 152,272 control chromosomes in the GnomAD database, including 143 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 0.038 (143 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.212

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0531 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: 0.0380 AC: 5788 AN: 152154 Hom.: 141 Cov.: 32

Gnomad AFR AF: 0.0113

Gnomad AMI AF: 0.0702

Gnomad AMR AF: 0.0380

Gnomad ASJ AF: 0.0397

Gnomad EAS AF: 0.000962

Gnomad SAS AF: 0.0478

Gnomad FIN AF: 0.0478

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0545

Gnomad OTH AF: 0.0340

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

GnomAD4 genome AF: 0.0381 AC: 5795 AN: 152272 Hom.: 143 Cov.: 32 AF XY: 0.0372 AC XY: 2773 AN XY: 74452

Gnomad4 AFR AF: 0.0113

Gnomad4 AMR AF: 0.0385

Gnomad4 ASJ AF: 0.0397

Gnomad4 EAS AF: 0.000964

Gnomad4 SAS AF: 0.0483

Gnomad4 FIN AF: 0.0478

Gnomad4 NFE AF: 0.0545

Gnomad4 OTH AF: 0.0336

Alfa AF: 0.0410 Hom.: 74

Bravo AF: 0.0360

Asia WGS AF: 0.0230 AC: 79 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
Cadd	Benign	1.8
Dann	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11688246; hg19: chr2-85705677;