chr1-181852272-C-T

Variant names:

• chr1-181852272-C-T
• rs4465155

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 0.252 in 151,636 control chromosomes in the GnomAD database, including 5,716 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 0.25 (5716 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.678

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.374 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: 0.252 AC: 38235 AN: 151518 Hom.: 5706 Cov.: 32

Gnomad AFR AF: 0.0837

Gnomad AMI AF: 0.297

Gnomad AMR AF: 0.304

Gnomad ASJ AF: 0.398

Gnomad EAS AF: 0.388

Gnomad SAS AF: 0.262

Gnomad FIN AF: 0.266

Gnomad MID AF: 0.207

Gnomad NFE AF: 0.322

Gnomad OTH AF: 0.252

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

GnomAD4 genome AF: 0.252 AC: 38259 AN: 151636 Hom.: 5716 Cov.: 32 AF XY: 0.253 AC XY: 18760 AN XY: 74070

Gnomad4 AFR AF: 0.0836

Gnomad4 AMR AF: 0.304

Gnomad4 ASJ AF: 0.398

Gnomad4 EAS AF: 0.388

Gnomad4 SAS AF: 0.262

Gnomad4 FIN AF: 0.266

Gnomad4 NFE AF: 0.322

Gnomad4 OTH AF: 0.260

Alfa AF: 0.276 Hom.: 2753

Bravo AF: 0.248

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.82
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4465155; hg19: chr1-181821407;