1-43005095-G-T

Variant names:

• chr1-43005095-G-T
• rs1754154

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 0.197 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
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.0721 AC: 2996 AN: 41526

American (AMR) AF: 0.155 AC: 2373 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.352 AC: 1221 AN: 3472

East Asian (EAS) AF: 0.00174 AC: 9 AN: 5186

South Asian (SAS) AF: 0.141 AC: 682 AN: 4820

European-Finnish (FIN) AF: 0.260 AC: 2748 AN: 10570

Middle Eastern (MID) AF: 0.228 AC: 67 AN: 294

European-Non Finnish (NFE) AF: 0.285 AC: 19383 AN: 67986

Other (OTH) AF: 0.195 AC: 412 AN: 2108

Alfa AF: 0.208 Hom.: 3393

Bravo AF: 0.183

Asia WGS AF: 0.0640 AC: 222 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.071
DANN	Benign	0.50
PhyloP100		-0.76

Splicing

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

Other links and lift over

dbSNP: rs1754154; hg19: chr1-43470766;