chr1-166564280-T-C

Position:

• chr1-166564280-T-C

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 0.268 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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.235

Gnomad4 AMR AF: 0.234

Gnomad4 ASJ AF: 0.252

Gnomad4 EAS AF: 0.312

Gnomad4 SAS AF: 0.208

Gnomad4 FIN AF: 0.280

Gnomad4 NFE AF: 0.296

Gnomad4 OTH AF: 0.243

Alfa AF: 0.276 Hom.: 1063

Bravo AF: 0.267

Asia WGS AF: 0.254 AC: 885 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs764024; hg19: chr1-166533517;