rs2509382

Variant names:

• chr11-91046275-G-C
• rs2509382

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.135 AC: 5585 AN: 41436

American (AMR) AF: 0.133 AC: 2018 AN: 15176

Ashkenazi Jewish (ASJ) AF: 0.171 AC: 592 AN: 3460

East Asian (EAS) AF: 0.104 AC: 530 AN: 5120

South Asian (SAS) AF: 0.131 AC: 631 AN: 4812

European-Finnish (FIN) AF: 0.137 AC: 1450 AN: 10556

Middle Eastern (MID) AF: 0.205 AC: 60 AN: 292

European-Non Finnish (NFE) AF: 0.153 AC: 10364 AN: 67854

Other (OTH) AF: 0.147 AC: 309 AN: 2106

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
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs2509382; hg19: chr11-90779443;