rs1109863

Positions:

• chr16-50658453-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 0.688 in 152,064 control chromosomes in the GnomAD database, including 36,518 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 0.69 (36518 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.440

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.716 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: 0.688 AC: 104501 AN: 151946 Hom.: 36504 Cov.: 32

Gnomad AFR AF: 0.688

Gnomad AMI AF: 0.808

Gnomad AMR AF: 0.614

Gnomad ASJ AF: 0.760

Gnomad EAS AF: 0.411

Gnomad SAS AF: 0.474

Gnomad FIN AF: 0.778

Gnomad MID AF: 0.734

Gnomad NFE AF: 0.721

Gnomad OTH AF: 0.678

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

GnomAD4 genome AF: 0.688 AC: 104577 AN: 152064 Hom.: 36518 Cov.: 32 AF XY: 0.684 AC XY: 50821 AN XY: 74332

Gnomad4 AFR AF: 0.688

Gnomad4 AMR AF: 0.613

Gnomad4 ASJ AF: 0.760

Gnomad4 EAS AF: 0.412

Gnomad4 SAS AF: 0.475

Gnomad4 FIN AF: 0.778

Gnomad4 NFE AF: 0.721

Gnomad4 OTH AF: 0.677

Alfa AF: 0.708 Hom.: 67949

Bravo AF: 0.675

Asia WGS AF: 0.469 AC: 1629 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	0.78
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1109863; hg19: chr16-50692364;