rs11648890

Positions:

• chr16-24362582-G-A

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 0.248 in 152,168 control chromosomes in the GnomAD database, including 4,868 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 0.25 (4847 hom., cov: 31)
  • Exomes 𝑓: 0.31 (21 hom.)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.548

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.342 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.248 AC: 37545 AN: 151614 Hom.: 4844 Cov.: 31

Gnomad AFR AF: 0.186

Gnomad AMI AF: 0.433

Gnomad AMR AF: 0.290

Gnomad ASJ AF: 0.269

Gnomad EAS AF: 0.356

Gnomad SAS AF: 0.264

Gnomad FIN AF: 0.309

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.253

Gnomad OTH AF: 0.263

GnomAD4 exome AF: 0.310 AC: 135 AN: 436 Hom.: 21 Cov.: 0 AF XY: 0.303 AC XY: 80 AN XY: 264

Gnomad4 FIN exome AF: 0.307

Gnomad4 NFE exome AF: 0.500

Gnomad4 OTH exome AF: 0.333

GnomAD4 genome AF: 0.248 AC: 37562 AN: 151732 Hom.: 4847 Cov.: 31 AF XY: 0.252 AC XY: 18657 AN XY: 74130

Gnomad4 AFR AF: 0.186

Gnomad4 AMR AF: 0.290

Gnomad4 ASJ AF: 0.269

Gnomad4 EAS AF: 0.355

Gnomad4 SAS AF: 0.263

Gnomad4 FIN AF: 0.309

Gnomad4 NFE AF: 0.253

Gnomad4 OTH AF: 0.259

Alfa AF: 0.253 Hom.: 5231

Bravo AF: 0.245

Asia WGS AF: 0.291 AC: 1011 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.7
DANN	Benign	0.29

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs11648890; hg19: chr16-24373903; COSMIC: COSV50073462;