rs16952847

Positions:

• chr18-51140499-A-C

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 0.0824 in 152,158 control chromosomes in the GnomAD database, including 1,555 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 0.082 (1555 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0880

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.265 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0824 AC: 12523 AN: 152040 Hom.: 1553 Cov.: 31

Gnomad AFR AF: 0.269

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0345

Gnomad ASJ AF: 0.0173

Gnomad EAS AF: 0.0494

Gnomad SAS AF: 0.00580

Gnomad FIN AF: 0.0146

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.00343

Gnomad OTH AF: 0.0535

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

GnomAD4 genome AF: 0.0824 AC: 12539 AN: 152158 Hom.: 1555 Cov.: 31 AF XY: 0.0817 AC XY: 6078 AN XY: 74412

Gnomad4 AFR AF: 0.269

Gnomad4 AMR AF: 0.0344

Gnomad4 ASJ AF: 0.0173

Gnomad4 EAS AF: 0.0493

Gnomad4 SAS AF: 0.00602

Gnomad4 FIN AF: 0.0146

Gnomad4 NFE AF: 0.00343

Gnomad4 OTH AF: 0.0530

Alfa AF: 0.0381 Hom.: 165

Bravo AF: 0.0920

Asia WGS AF: 0.0440 AC: 153 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.2
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16952847; hg19: chr18-48666869;