rs11643520

Variant names:

• chr16-24520397-T-C
• rs11643520

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 0.0775 in 152,200 control chromosomes in the GnomAD database, including 654 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 0.078 (654 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.641

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.147 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: 0.0776 AC: 11803 AN: 152082 Hom.: 657 Cov.: 32

Gnomad AFR AF: 0.0192

Gnomad AMI AF: 0.113

Gnomad AMR AF: 0.103

Gnomad ASJ AF: 0.174

Gnomad EAS AF: 0.00385

Gnomad SAS AF: 0.156

Gnomad FIN AF: 0.0431

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.108

Gnomad OTH AF: 0.0750

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

GnomAD4 genome AF: 0.0775 AC: 11797 AN: 152200 Hom.: 654 Cov.: 32 AF XY: 0.0761 AC XY: 5659 AN XY: 74410

Gnomad4 AFR AF: 0.0191

Gnomad4 AMR AF: 0.103

Gnomad4 ASJ AF: 0.174

Gnomad4 EAS AF: 0.00386

Gnomad4 SAS AF: 0.156

Gnomad4 FIN AF: 0.0431

Gnomad4 NFE AF: 0.108

Gnomad4 OTH AF: 0.0743

Alfa AF: 0.105 Hom.: 1452

Bravo AF: 0.0760

Asia WGS AF: 0.0640 AC: 222 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.46
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11643520; hg19: chr16-24531718;