rs2509382

Positions:

• chr11-91046275-G-C

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 0.143 in 151,724 control chromosomes in the GnomAD database, including 1,558 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 0.14 (1558 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.61

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.15 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.143 AC: 21706 AN: 151606 Hom.: 1553 Cov.: 32

Gnomad AFR AF: 0.135

Gnomad AMI AF: 0.209

Gnomad AMR AF: 0.133

Gnomad ASJ AF: 0.171

Gnomad EAS AF: 0.104

Gnomad SAS AF: 0.131

Gnomad FIN AF: 0.137

Gnomad MID AF: 0.207

Gnomad NFE AF: 0.153

Gnomad OTH AF: 0.140

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

GnomAD4 genome AF: 0.143 AC: 21730 AN: 151724 Hom.: 1558 Cov.: 32 AF XY: 0.142 AC XY: 10549 AN XY: 74144

Gnomad4 AFR AF: 0.135

Gnomad4 AMR AF: 0.133

Gnomad4 ASJ AF: 0.171

Gnomad4 EAS AF: 0.104

Gnomad4 SAS AF: 0.131

Gnomad4 FIN AF: 0.137

Gnomad4 NFE AF: 0.153

Gnomad4 OTH AF: 0.147

Alfa AF: 0.148 Hom.: 222

Bravo AF: 0.144

Asia WGS AF: 0.140 AC: 488 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.48
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2509382; hg19: chr11-90779443;