rs16953030

Positions:

• chr18-51263449-A-G

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 0.0656 in 152,186 control chromosomes in the GnomAD database, including 701 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 0.066 (701 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.942

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.169 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: 0.0655 AC: 9955 AN: 152068 Hom.: 694 Cov.: 32

Gnomad AFR AF: 0.172

Gnomad AMI AF: 0.0363

Gnomad AMR AF: 0.0345

Gnomad ASJ AF: 0.0375

Gnomad EAS AF: 0.110

Gnomad SAS AF: 0.0405

Gnomad FIN AF: 0.0245

Gnomad MID AF: 0.0669

Gnomad NFE AF: 0.0146

Gnomad OTH AF: 0.0535

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

GnomAD4 genome AF: 0.0656 AC: 9990 AN: 152186 Hom.: 701 Cov.: 32 AF XY: 0.0658 AC XY: 4897 AN XY: 74404

Gnomad4 AFR AF: 0.172

Gnomad4 AMR AF: 0.0345

Gnomad4 ASJ AF: 0.0375

Gnomad4 EAS AF: 0.110

Gnomad4 SAS AF: 0.0397

Gnomad4 FIN AF: 0.0245

Gnomad4 NFE AF: 0.0146

Gnomad4 OTH AF: 0.0549

Alfa AF: 0.0287 Hom.: 86

Bravo AF: 0.0703

Asia WGS AF: 0.0830 AC: 289 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.24
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16953030; hg19: chr18-48789819;