11-2320502-T-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 0.702 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.562

Gnomad4 AMR AF: 0.692

Gnomad4 ASJ AF: 0.712

Gnomad4 EAS AF: 0.420

Gnomad4 SAS AF: 0.719

Gnomad4 FIN AF: 0.682

Gnomad4 NFE AF: 0.809

Gnomad4 OTH AF: 0.729

Alfa AF: 0.788 Hom.: 62400

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2651843; hg19: chr11-2341732;