rs16912285

Variant names:

• chr11-24230982-A-G
• rs16912285

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 0.0973 in 152,262 control chromosomes in the GnomAD database, including 865 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 0.097 (865 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0380

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.195 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: 0.0973 AC: 14803 AN: 152144 Hom.: 862 Cov.: 32

Gnomad AFR AF: 0.0548

Gnomad AMI AF: 0.0855

Gnomad AMR AF: 0.157

Gnomad ASJ AF: 0.143

Gnomad EAS AF: 0.133

Gnomad SAS AF: 0.205

Gnomad FIN AF: 0.0667

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.101

Gnomad OTH AF: 0.113

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

GnomAD4 genome AF: 0.0973 AC: 14808 AN: 152262 Hom.: 865 Cov.: 32 AF XY: 0.0997 AC XY: 7420 AN XY: 74442

Gnomad4 AFR AF: 0.0546

Gnomad4 AMR AF: 0.157

Gnomad4 ASJ AF: 0.143

Gnomad4 EAS AF: 0.132

Gnomad4 SAS AF: 0.206

Gnomad4 FIN AF: 0.0667

Gnomad4 NFE AF: 0.101

Gnomad4 OTH AF: 0.112

Alfa AF: 0.102 Hom.: 712

Bravo AF: 0.0999

Asia WGS AF: 0.158 AC: 548 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.92
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16912285; hg19: chr11-24252528;