1-176454004-C-T

Position:

• chr1-176454004-C-T

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;