1-43005095-G-T

Variant names:

• chr1-43005095-G-T
• rs1754154

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 0.197 in 152,156 control chromosomes in the GnomAD database, including 3,794 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 0.20 (3794 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.763

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.282 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: 0.197 AC: 30004 AN: 152038 Hom.: 3793 Cov.: 32

Gnomad AFR AF: 0.0724

Gnomad AMI AF: 0.122

Gnomad AMR AF: 0.156

Gnomad ASJ AF: 0.352

Gnomad EAS AF: 0.00173

Gnomad SAS AF: 0.141

Gnomad FIN AF: 0.260

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.285

Gnomad OTH AF: 0.199

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

GnomAD4 genome AF: 0.197 AC: 30002 AN: 152156 Hom.: 3794 Cov.: 32 AF XY: 0.191 AC XY: 14188 AN XY: 74374

Gnomad4 AFR AF: 0.0721

Gnomad4 AMR AF: 0.155

Gnomad4 ASJ AF: 0.352

Gnomad4 EAS AF: 0.00174

Gnomad4 SAS AF: 0.141

Gnomad4 FIN AF: 0.260

Gnomad4 NFE AF: 0.285

Gnomad4 OTH AF: 0.195

Alfa AF: 0.227 Hom.: 2414

Bravo AF: 0.183

Asia WGS AF: 0.0640 AC: 222 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.071
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1754154; hg19: chr1-43470766;