chr1-182623201-C-T

Variant names:

• chr1-182623201-C-T
• rs528846

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 0.169 in 152,008 control chromosomes in the GnomAD database, including 3,104 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 0.17 (3104 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.782

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.342 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: 0.168 AC: 25587 AN: 151890 Hom.: 3087 Cov.: 32

Gnomad AFR AF: 0.346

Gnomad AMI AF: 0.162

Gnomad AMR AF: 0.0928

Gnomad ASJ AF: 0.0769

Gnomad EAS AF: 0.0399

Gnomad SAS AF: 0.0584

Gnomad FIN AF: 0.127

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.108

Gnomad OTH AF: 0.139

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

GnomAD4 genome AF: 0.169 AC: 25644 AN: 152008 Hom.: 3104 Cov.: 32 AF XY: 0.166 AC XY: 12309 AN XY: 74264

Gnomad4 AFR AF: 0.346

Gnomad4 AMR AF: 0.0926

Gnomad4 ASJ AF: 0.0769

Gnomad4 EAS AF: 0.0402

Gnomad4 SAS AF: 0.0580

Gnomad4 FIN AF: 0.127

Gnomad4 NFE AF: 0.108

Gnomad4 OTH AF: 0.138

Alfa AF: 0.116 Hom.: 1938

Bravo AF: 0.174

Asia WGS AF: 0.0750 AC: 262 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.4
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs528846; hg19: chr1-182592336; COSMIC: COSV59995903;