chr16-25614955-A-G

Variant names:

• chr16-25614955-A-G
• rs508414

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 0.218 in 152,088 control chromosomes in the GnomAD database, including 3,738 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 0.22 (3738 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.964
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.63).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.282 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.217 AC: 33041 AN: 151970 Hom.: 3722 Cov.: 32

Gnomad AFR AF: 0.286

Gnomad AMI AF: 0.0746

Gnomad AMR AF: 0.155

Gnomad ASJ AF: 0.183

Gnomad EAS AF: 0.199

Gnomad SAS AF: 0.241

Gnomad FIN AF: 0.216

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.194

Gnomad OTH AF: 0.202

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

GnomAD4 genome AF: 0.218 AC: 33095 AN: 152088 Hom.: 3738 Cov.: 32 AF XY: 0.217 AC XY: 16123 AN XY: 74338

African (AFR) AF: 0.286 AC: 11875 AN: 41486

American (AMR) AF: 0.155 AC: 2369 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.183 AC: 633 AN: 3468

East Asian (EAS) AF: 0.199 AC: 1030 AN: 5170

South Asian (SAS) AF: 0.241 AC: 1161 AN: 4818

European-Finnish (FIN) AF: 0.216 AC: 2285 AN: 10562

Middle Eastern (MID) AF: 0.187 AC: 55 AN: 294

European-Non Finnish (NFE) AF: 0.194 AC: 13195 AN: 67982

Other (OTH) AF: 0.202 AC: 424 AN: 2104

Alfa AF: 0.196 Hom.: 2061

Bravo AF: 0.212

Asia WGS AF: 0.208 AC: 725 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.63
CADD	Benign	0.36
DANN	Benign	0.68
PhyloP100		-0.96

Splicing

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

Other links and lift over

dbSNP: rs508414; hg19: chr16-25626276;