rs16913724

Variant names:

• chr11-88248111-A-G
• rs16913724

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 0.123 in 152,252 control chromosomes in the GnomAD database, including 1,491 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 0.12 (1491 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.62

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.224 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: 0.123 AC: 18664 AN: 152134 Hom.: 1485 Cov.: 32

Gnomad AFR AF: 0.0387

Gnomad AMI AF: 0.0406

Gnomad AMR AF: 0.230

Gnomad ASJ AF: 0.105

Gnomad EAS AF: 0.177

Gnomad SAS AF: 0.190

Gnomad FIN AF: 0.137

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.141

Gnomad OTH AF: 0.125

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

GnomAD4 genome AF: 0.123 AC: 18671 AN: 152252 Hom.: 1491 Cov.: 32 AF XY: 0.127 AC XY: 9460 AN XY: 74456

Gnomad4 AFR AF: 0.0386

Gnomad4 AMR AF: 0.230

Gnomad4 ASJ AF: 0.105

Gnomad4 EAS AF: 0.177

Gnomad4 SAS AF: 0.190

Gnomad4 FIN AF: 0.137

Gnomad4 NFE AF: 0.141

Gnomad4 OTH AF: 0.124

Alfa AF: 0.138 Hom.: 1519

Bravo AF: 0.126

Asia WGS AF: 0.167 AC: 580 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	9.8
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16913724; hg19: chr11-87981279;