rs16952847

Variant names:

• chr18-51140499-A-C
• rs16952847

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.269 AC: 11162 AN: 41480

American (AMR) AF: 0.0344 AC: 526 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0173 AC: 60 AN: 3470

East Asian (EAS) AF: 0.0493 AC: 255 AN: 5168

South Asian (SAS) AF: 0.00602 AC: 29 AN: 4820

European-Finnish (FIN) AF: 0.0146 AC: 155 AN: 10602

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.00343 AC: 233 AN: 68008

Other (OTH) AF: 0.0530 AC: 112 AN: 2114

Alfa AF: 0.0352 Hom.: 227

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
PhyloP100		-0.088

Splicing

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

Other links and lift over

dbSNP: rs16952847; hg19: chr18-48666869;