rs16825675

Variant names:

• chr1-186646863-T-C
• rs16825675

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 0.368 in 151,972 control chromosomes in the GnomAD database, including 11,959 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 0.37 (11959 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.822
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.581 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: 0.367 AC: 55766 AN: 151854 Hom.: 11907 Cov.: 32

Gnomad AFR AF: 0.587

Gnomad AMI AF: 0.248

Gnomad AMR AF: 0.391

Gnomad ASJ AF: 0.315

Gnomad EAS AF: 0.477

Gnomad SAS AF: 0.255

Gnomad FIN AF: 0.214

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.257

Gnomad OTH AF: 0.369

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

GnomAD4 genome AF: 0.368 AC: 55875 AN: 151972 Hom.: 11959 Cov.: 32 AF XY: 0.365 AC XY: 27093 AN XY: 74298

African (AFR) AF: 0.587 AC: 24327 AN: 41420

American (AMR) AF: 0.392 AC: 5974 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.315 AC: 1092 AN: 3472

East Asian (EAS) AF: 0.476 AC: 2464 AN: 5172

South Asian (SAS) AF: 0.254 AC: 1222 AN: 4820

European-Finnish (FIN) AF: 0.214 AC: 2256 AN: 10554

Middle Eastern (MID) AF: 0.286 AC: 84 AN: 294

European-Non Finnish (NFE) AF: 0.257 AC: 17442 AN: 67968

Other (OTH) AF: 0.373 AC: 788 AN: 2110

Alfa AF: 0.328 Hom.: 1691

Bravo AF: 0.397

Asia WGS AF: 0.414 AC: 1435 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.99
DANN	Benign	0.33
PhyloP100		-0.82

Splicing

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

Other links and lift over

dbSNP: rs16825675; hg19: chr1-186615995;