1-176454004-C-T

Variant names:

• chr1-176454004-C-T
• rs4471226

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 0.83 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.830 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

Gnomad4 AFR AF: 0.603

Gnomad4 AMR AF: 0.900

Gnomad4 ASJ AF: 0.901

Gnomad4 EAS AF: 0.901

Gnomad4 SAS AF: 0.813

Gnomad4 FIN AF: 0.962

Gnomad4 NFE AF: 0.921

Gnomad4 OTH AF: 0.865

Alfa AF: 0.903 Hom.: 58985

Bravo AF: 0.817

Asia WGS AF: 0.852 AC: 2964 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4471226; hg19: chr1-176423140;