1-54531340-C-T

Variant names:

• chr1-54531340-C-T
• rs11584093

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 0.842 in 152,094 control chromosomes in the GnomAD database, including 54,224 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 0.84 (54224 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.656
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.928 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: 0.841 AC: 127884 AN: 151976 Hom.: 54175 Cov.: 30

Gnomad AFR AF: 0.936

Gnomad AMI AF: 0.912

Gnomad AMR AF: 0.826

Gnomad ASJ AF: 0.858

Gnomad EAS AF: 0.878

Gnomad SAS AF: 0.820

Gnomad FIN AF: 0.773

Gnomad MID AF: 0.921

Gnomad NFE AF: 0.794

Gnomad OTH AF: 0.858

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

GnomAD4 genome AF: 0.842 AC: 127996 AN: 152094 Hom.: 54224 Cov.: 30 AF XY: 0.840 AC XY: 62422 AN XY: 74346

African (AFR) AF: 0.936 AC: 38833 AN: 41510

American (AMR) AF: 0.826 AC: 12609 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.858 AC: 2980 AN: 3472

East Asian (EAS) AF: 0.878 AC: 4530 AN: 5158

South Asian (SAS) AF: 0.820 AC: 3956 AN: 4824

European-Finnish (FIN) AF: 0.773 AC: 8157 AN: 10556

Middle Eastern (MID) AF: 0.925 AC: 272 AN: 294

European-Non Finnish (NFE) AF: 0.794 AC: 54021 AN: 68004

Other (OTH) AF: 0.857 AC: 1808 AN: 2110

Alfa AF: 0.812 Hom.: 45320

Bravo AF: 0.854

Asia WGS AF: 0.842 AC: 2928 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.49
DANN	Benign	0.65
PhyloP100		-0.66

Splicing

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

Other links and lift over

dbSNP: rs11584093; hg19: chr1-54997013;