chr1-159212305-C-T

Variant names:

• chr1-159212305-C-T
• rs3027045

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 0.441 in 151,924 control chromosomes in the GnomAD database, including 15,446 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 0.44 (15446 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.411
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.576 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.441 AC: 66878 AN: 151806 Hom.: 15435 Cov.: 31

Gnomad AFR AF: 0.583

Gnomad AMI AF: 0.416

Gnomad AMR AF: 0.418

Gnomad ASJ AF: 0.424

Gnomad EAS AF: 0.484

Gnomad SAS AF: 0.386

Gnomad FIN AF: 0.401

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.368

Gnomad OTH AF: 0.417

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

GnomAD4 genome AF: 0.441 AC: 66923 AN: 151924 Hom.: 15446 Cov.: 31 AF XY: 0.441 AC XY: 32727 AN XY: 74250

African (AFR) AF: 0.582 AC: 24095 AN: 41386

American (AMR) AF: 0.418 AC: 6388 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.424 AC: 1470 AN: 3470

East Asian (EAS) AF: 0.483 AC: 2488 AN: 5146

South Asian (SAS) AF: 0.386 AC: 1860 AN: 4820

European-Finnish (FIN) AF: 0.401 AC: 4238 AN: 10556

Middle Eastern (MID) AF: 0.446 AC: 131 AN: 294

European-Non Finnish (NFE) AF: 0.368 AC: 25007 AN: 67968

Other (OTH) AF: 0.413 AC: 869 AN: 2102

Alfa AF: 0.422 Hom.: 3116

Bravo AF: 0.450

Asia WGS AF: 0.419 AC: 1457 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	8.1
DANN	Benign	0.75
PhyloP100		0.41

Splicing

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

Other links and lift over

dbSNP: rs3027045; hg19: chr1-159182095;