chr1-166564280-T-C

Variant names:

• chr1-166564280-T-C
• rs764024

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 0.268 in 152,078 control chromosomes in the GnomAD database, including 5,624 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 0.27 (5624 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0170
• Publications: 2 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 (EAS) allele frequency at 95% confidence interval = 0.299 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: 0.268 AC: 40760 AN: 151962 Hom.: 5628 Cov.: 32

Gnomad AFR AF: 0.236

Gnomad AMI AF: 0.293

Gnomad AMR AF: 0.235

Gnomad ASJ AF: 0.252

Gnomad EAS AF: 0.311

Gnomad SAS AF: 0.208

Gnomad FIN AF: 0.280

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.296

Gnomad OTH AF: 0.241

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

GnomAD4 genome AF: 0.268 AC: 40774 AN: 152078 Hom.: 5624 Cov.: 32 AF XY: 0.264 AC XY: 19654 AN XY: 74332

African (AFR) AF: 0.235 AC: 9766 AN: 41478

American (AMR) AF: 0.234 AC: 3580 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.252 AC: 873 AN: 3470

East Asian (EAS) AF: 0.312 AC: 1612 AN: 5172

South Asian (SAS) AF: 0.208 AC: 1001 AN: 4818

European-Finnish (FIN) AF: 0.280 AC: 2961 AN: 10574

Middle Eastern (MID) AF: 0.194 AC: 57 AN: 294

European-Non Finnish (NFE) AF: 0.296 AC: 20144 AN: 67972

Other (OTH) AF: 0.243 AC: 514 AN: 2114

Alfa AF: 0.274 Hom.: 2042

Bravo AF: 0.267

Asia WGS AF: 0.254 AC: 885 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.9
DANN	Benign	0.72
PhyloP100		0.017

Splicing

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

Other links and lift over

dbSNP: rs764024; hg19: chr1-166533517; COSMIC: COSV107524440;