rs1452554

Variant names:

• chr4-18918541-C-T
• rs1452554

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 0.409 in 151,794 control chromosomes in the GnomAD database, including 12,873 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 0.41 (12873 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.741
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.609 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.409 AC: 62059 AN: 151676 Hom.: 12848 Cov.: 31

Gnomad AFR AF: 0.385

Gnomad AMI AF: 0.263

Gnomad AMR AF: 0.446

Gnomad ASJ AF: 0.505

Gnomad EAS AF: 0.626

Gnomad SAS AF: 0.490

Gnomad FIN AF: 0.379

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.394

Gnomad OTH AF: 0.442

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

GnomAD4 genome AF: 0.409 AC: 62122 AN: 151794 Hom.: 12873 Cov.: 31 AF XY: 0.415 AC XY: 30745 AN XY: 74142

African (AFR) AF: 0.385 AC: 15934 AN: 41392

American (AMR) AF: 0.446 AC: 6773 AN: 15194

Ashkenazi Jewish (ASJ) AF: 0.505 AC: 1750 AN: 3464

East Asian (EAS) AF: 0.627 AC: 3232 AN: 5158

South Asian (SAS) AF: 0.489 AC: 2356 AN: 4818

European-Finnish (FIN) AF: 0.379 AC: 3995 AN: 10550

Middle Eastern (MID) AF: 0.442 AC: 129 AN: 292

European-Non Finnish (NFE) AF: 0.394 AC: 26771 AN: 67906

Other (OTH) AF: 0.447 AC: 942 AN: 2108

Alfa AF: 0.400 Hom.: 6979

Bravo AF: 0.413

Asia WGS AF: 0.540 AC: 1877 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.78
DANN	Benign	0.69
PhyloP100		-0.74

Splicing

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

Other links and lift over

dbSNP: rs1452554; hg19: chr4-18920164;