1-54018809-C-T

Variant names:

• chr1-54018809-C-T
• rs914720

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 0.455 in 151,820 control chromosomes in the GnomAD database, including 16,021 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 0.45 (16021 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.100
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.605 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: 0.455 AC: 68993 AN: 151702 Hom.: 16008 Cov.: 31

Gnomad AFR AF: 0.495

Gnomad AMI AF: 0.597

Gnomad AMR AF: 0.508

Gnomad ASJ AF: 0.554

Gnomad EAS AF: 0.623

Gnomad SAS AF: 0.331

Gnomad FIN AF: 0.347

Gnomad MID AF: 0.566

Gnomad NFE AF: 0.422

Gnomad OTH AF: 0.517

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

GnomAD4 genome AF: 0.455 AC: 69048 AN: 151820 Hom.: 16021 Cov.: 31 AF XY: 0.453 AC XY: 33577 AN XY: 74160

African (AFR) AF: 0.495 AC: 20477 AN: 41378

American (AMR) AF: 0.508 AC: 7758 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.554 AC: 1920 AN: 3468

East Asian (EAS) AF: 0.623 AC: 3204 AN: 5146

South Asian (SAS) AF: 0.330 AC: 1589 AN: 4812

European-Finnish (FIN) AF: 0.347 AC: 3649 AN: 10514

Middle Eastern (MID) AF: 0.551 AC: 162 AN: 294

European-Non Finnish (NFE) AF: 0.422 AC: 28662 AN: 67932

Other (OTH) AF: 0.514 AC: 1084 AN: 2108

Alfa AF: 0.448 Hom.: 5159

Bravo AF: 0.476

Asia WGS AF: 0.449 AC: 1564 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	11
DANN	Benign	0.84
PhyloP100		0.10

Splicing

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

Other links and lift over

dbSNP: rs914720; hg19: chr1-54484482;