rs16924750

Variant names:

• chr11-13163679-G-A
• rs16924750

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 0.232 in 152,044 control chromosomes in the GnomAD database, including 7,903 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 0.23 (7903 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.146

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.583 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: 0.232 AC: 35259 AN: 151926 Hom.: 7896 Cov.: 32

Gnomad AFR AF: 0.590

Gnomad AMI AF: 0.0351

Gnomad AMR AF: 0.134

Gnomad ASJ AF: 0.114

Gnomad EAS AF: 0.0838

Gnomad SAS AF: 0.112

Gnomad FIN AF: 0.0519

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.0945

Gnomad OTH AF: 0.205

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

GnomAD4 genome AF: 0.232 AC: 35303 AN: 152044 Hom.: 7903 Cov.: 32 AF XY: 0.225 AC XY: 16737 AN XY: 74314

Gnomad4 AFR AF: 0.589

Gnomad4 AMR AF: 0.133

Gnomad4 ASJ AF: 0.114

Gnomad4 EAS AF: 0.0838

Gnomad4 SAS AF: 0.110

Gnomad4 FIN AF: 0.0519

Gnomad4 NFE AF: 0.0946

Gnomad4 OTH AF: 0.204

Alfa AF: 0.113 Hom.: 3159

Bravo AF: 0.252

Asia WGS AF: 0.122 AC: 421 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.80
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16924750; hg19: chr11-13185226;