rs16953030

Variant names:

• chr18-51263449-A-G
• rs16953030

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 0.0656 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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.172 AC: 7155 AN: 41486

American (AMR) AF: 0.0345 AC: 527 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0375 AC: 130 AN: 3470

East Asian (EAS) AF: 0.110 AC: 568 AN: 5178

South Asian (SAS) AF: 0.0397 AC: 191 AN: 4814

European-Finnish (FIN) AF: 0.0245 AC: 260 AN: 10616

Middle Eastern (MID) AF: 0.0651 AC: 19 AN: 292

European-Non Finnish (NFE) AF: 0.0146 AC: 991 AN: 68018

Other (OTH) AF: 0.0549 AC: 116 AN: 2114

Alfa AF: 0.0364 Hom.: 678

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
PhyloP100		-0.94

Splicing

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

Other links and lift over

dbSNP: rs16953030; hg19: chr18-48789819;