rs16951664

Variant names:

• chr18-7386870-G-T
• rs16951664

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 0.474 in 151,852 control chromosomes in the GnomAD database, including 17,309 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 0.47 (17309 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0800
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.501 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.474 AC: 71914 AN: 151734 Hom.: 17300 Cov.: 30

Gnomad AFR AF: 0.387

Gnomad AMI AF: 0.624

Gnomad AMR AF: 0.506

Gnomad ASJ AF: 0.622

Gnomad EAS AF: 0.512

Gnomad SAS AF: 0.455

Gnomad FIN AF: 0.485

Gnomad MID AF: 0.620

Gnomad NFE AF: 0.505

Gnomad OTH AF: 0.506

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

GnomAD4 genome AF: 0.474 AC: 71962 AN: 151852 Hom.: 17309 Cov.: 30 AF XY: 0.474 AC XY: 35151 AN XY: 74186

African (AFR) AF: 0.387 AC: 16029 AN: 41416

American (AMR) AF: 0.506 AC: 7716 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.622 AC: 2156 AN: 3464

East Asian (EAS) AF: 0.512 AC: 2640 AN: 5156

South Asian (SAS) AF: 0.454 AC: 2188 AN: 4818

European-Finnish (FIN) AF: 0.485 AC: 5086 AN: 10490

Middle Eastern (MID) AF: 0.616 AC: 181 AN: 294

European-Non Finnish (NFE) AF: 0.505 AC: 34331 AN: 67940

Other (OTH) AF: 0.506 AC: 1067 AN: 2110

Alfa AF: 0.499 Hom.: 57221

Bravo AF: 0.472

Asia WGS AF: 0.475 AC: 1649 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.6
DANN	Benign	0.45
PhyloP100		0.080

Splicing

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

Other links and lift over

dbSNP: rs16951664; hg19: chr18-7386868;