rs11684747

chr2-9557042-A-G

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 0.185 in 152,122 control chromosomes in the GnomAD database, including 2,746 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 0.19 (2746 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.107

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.203 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: 0.185 AC: 28148 AN: 152004 Hom.: 2742 Cov.: 32

Gnomad AFR AF: 0.191

Gnomad AMI AF: 0.391

Gnomad AMR AF: 0.154

Gnomad ASJ AF: 0.238

Gnomad EAS AF: 0.0250

Gnomad SAS AF: 0.0964

Gnomad FIN AF: 0.151

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.206

Gnomad OTH AF: 0.207

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

GnomAD4 genome AF: 0.185 AC: 28173 AN: 152122 Hom.: 2746 Cov.: 32 AF XY: 0.181 AC XY: 13445 AN XY: 74386

Gnomad4 AFR AF: 0.191

Gnomad4 AMR AF: 0.154

Gnomad4 ASJ AF: 0.238

Gnomad4 EAS AF: 0.0249

Gnomad4 SAS AF: 0.0962

Gnomad4 FIN AF: 0.151

Gnomad4 NFE AF: 0.206

Gnomad4 OTH AF: 0.204

Alfa AF: 0.205 Hom.: 3161

Bravo AF: 0.190

Asia WGS AF: 0.0920 AC: 322 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	4.1
Dann	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11684747; hg19: chr2-9697171;