1-176454004-C-T

Variant names:

• chr1-176454004-C-T
• rs4471226

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 0.83 in 152,134 control chromosomes in the GnomAD database, including 53,955 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 0.83 (53955 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.51
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.915 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: 0.830 AC: 126241 AN: 152016 Hom.: 53942 Cov.: 31

Gnomad AFR AF: 0.604

Gnomad AMI AF: 0.964

Gnomad AMR AF: 0.900

Gnomad ASJ AF: 0.901

Gnomad EAS AF: 0.902

Gnomad SAS AF: 0.813

Gnomad FIN AF: 0.962

Gnomad MID AF: 0.899

Gnomad NFE AF: 0.921

Gnomad OTH AF: 0.864

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

GnomAD4 genome AF: 0.830 AC: 126291 AN: 152134 Hom.: 53955 Cov.: 31 AF XY: 0.832 AC XY: 61839 AN XY: 74366

African (AFR) AF: 0.603 AC: 25012 AN: 41454

American (AMR) AF: 0.900 AC: 13737 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.901 AC: 3129 AN: 3472

East Asian (EAS) AF: 0.901 AC: 4651 AN: 5162

South Asian (SAS) AF: 0.813 AC: 3919 AN: 4822

European-Finnish (FIN) AF: 0.962 AC: 10210 AN: 10618

Middle Eastern (MID) AF: 0.895 AC: 263 AN: 294

European-Non Finnish (NFE) AF: 0.921 AC: 62667 AN: 68028

Other (OTH) AF: 0.865 AC: 1826 AN: 2112

Alfa AF: 0.889 Hom.: 85249

Bravo AF: 0.817

Asia WGS AF: 0.852 AC: 2964 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.16
DANN	Benign	0.63
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs4471226; hg19: chr1-176423140;