11-2320502-T-C

Variant names:

• chr11-2320502-T-C
• rs2651843

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 0.702 in 152,158 control chromosomes in the GnomAD database, including 38,556 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 0.70 (38556 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.56
• Publications: 13 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.803 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: 0.702 AC: 106680 AN: 152040 Hom.: 38520 Cov.: 34

Gnomad AFR AF: 0.562

Gnomad AMI AF: 0.863

Gnomad AMR AF: 0.692

Gnomad ASJ AF: 0.712

Gnomad EAS AF: 0.420

Gnomad SAS AF: 0.719

Gnomad FIN AF: 0.682

Gnomad MID AF: 0.661

Gnomad NFE AF: 0.809

Gnomad OTH AF: 0.728

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

GnomAD4 genome AF: 0.702 AC: 106766 AN: 152158 Hom.: 38556 Cov.: 34 AF XY: 0.695 AC XY: 51676 AN XY: 74386

African (AFR) AF: 0.562 AC: 23336 AN: 41508

American (AMR) AF: 0.692 AC: 10583 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.712 AC: 2472 AN: 3470

East Asian (EAS) AF: 0.420 AC: 2169 AN: 5170

South Asian (SAS) AF: 0.719 AC: 3465 AN: 4820

European-Finnish (FIN) AF: 0.682 AC: 7231 AN: 10596

Middle Eastern (MID) AF: 0.656 AC: 193 AN: 294

European-Non Finnish (NFE) AF: 0.809 AC: 54990 AN: 67984

Other (OTH) AF: 0.729 AC: 1543 AN: 2116

Alfa AF: 0.776 Hom.: 84522

Bravo AF: 0.695

Asia WGS AF: 0.653 AC: 2275 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.2
DANN	Benign	0.56
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs2651843; hg19: chr11-2341732;