rs16825675

Variant names:

• chr1-186646863-T-C
• rs16825675

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 0.368 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.367 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

Gnomad4 AFR AF: 0.587

Gnomad4 AMR AF: 0.392

Gnomad4 ASJ AF: 0.315

Gnomad4 EAS AF: 0.476

Gnomad4 SAS AF: 0.254

Gnomad4 FIN AF: 0.214

Gnomad4 NFE AF: 0.257

Gnomad4 OTH AF: 0.373

Alfa AF: 0.322 Hom.: 1574

Bravo AF: 0.397

Asia WGS AF: 0.414 AC: 1435 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16825675; hg19: chr1-186615995;