11-82822586-T-C

Variant names:

• chr11-82822586-T-C
• rs586607

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 0.511 in 152,066 control chromosomes in the GnomAD database, including 21,841 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 0.51 (21841 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.217
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.735 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: 0.511 AC: 77570 AN: 151948 Hom.: 21790 Cov.: 32

Gnomad AFR AF: 0.741

Gnomad AMI AF: 0.230

Gnomad AMR AF: 0.516

Gnomad ASJ AF: 0.349

Gnomad EAS AF: 0.730

Gnomad SAS AF: 0.534

Gnomad FIN AF: 0.366

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.386

Gnomad OTH AF: 0.485

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

GnomAD4 genome AF: 0.511 AC: 77684 AN: 152066 Hom.: 21841 Cov.: 32 AF XY: 0.513 AC XY: 38126 AN XY: 74338

African (AFR) AF: 0.742 AC: 30747 AN: 41452

American (AMR) AF: 0.516 AC: 7887 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.349 AC: 1211 AN: 3470

East Asian (EAS) AF: 0.730 AC: 3781 AN: 5180

South Asian (SAS) AF: 0.534 AC: 2577 AN: 4824

European-Finnish (FIN) AF: 0.366 AC: 3856 AN: 10548

Middle Eastern (MID) AF: 0.442 AC: 130 AN: 294

European-Non Finnish (NFE) AF: 0.386 AC: 26261 AN: 67980

Other (OTH) AF: 0.484 AC: 1024 AN: 2114

Alfa AF: 0.439 Hom.: 5847

Bravo AF: 0.529

Asia WGS AF: 0.606 AC: 2107 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	6.3
DANN	Benign	0.77
PhyloP100		-0.22

Splicing

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

Other links and lift over

dbSNP: rs586607; hg19: chr11-82533628;