16-11192833-A-G

Variant names:

• chr16-11192833-A-G
• rs248836

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 0.462 in 152,082 control chromosomes in the GnomAD database, including 17,409 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 0.46 (17409 hom., cov: 33)
• 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=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.624 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: 0.462 AC: 70236 AN: 151964 Hom.: 17370 Cov.: 33

Gnomad AFR AF: 0.630

Gnomad AMI AF: 0.421

Gnomad AMR AF: 0.328

Gnomad ASJ AF: 0.320

Gnomad EAS AF: 0.531

Gnomad SAS AF: 0.269

Gnomad FIN AF: 0.498

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.403

Gnomad OTH AF: 0.433

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

GnomAD4 genome AF: 0.462 AC: 70321 AN: 152082 Hom.: 17409 Cov.: 33 AF XY: 0.461 AC XY: 34289 AN XY: 74330

Gnomad4 AFR AF: 0.630

Gnomad4 AMR AF: 0.327

Gnomad4 ASJ AF: 0.320

Gnomad4 EAS AF: 0.532

Gnomad4 SAS AF: 0.269

Gnomad4 FIN AF: 0.498

Gnomad4 NFE AF: 0.403

Gnomad4 OTH AF: 0.435

Alfa AF: 0.383 Hom.: 5336

Bravo AF: 0.459

Asia WGS AF: 0.411 AC: 1425 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.35
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs248836; hg19: chr16-11286690;