rs1454909

Variant names:

• chr5-57956571-C-T
• rs1454909

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 0.495 in 151,790 control chromosomes in the GnomAD database, including 19,926 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 0.49 (19926 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.13

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.594 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: 0.495 AC: 75146 AN: 151672 Hom.: 19942 Cov.: 32

Gnomad AFR AF: 0.308

Gnomad AMI AF: 0.514

Gnomad AMR AF: 0.483

Gnomad ASJ AF: 0.627

Gnomad EAS AF: 0.380

Gnomad SAS AF: 0.613

Gnomad FIN AF: 0.583

Gnomad MID AF: 0.668

Gnomad NFE AF: 0.591

Gnomad OTH AF: 0.518

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

GnomAD4 genome AF: 0.495 AC: 75134 AN: 151790 Hom.: 19926 Cov.: 32 AF XY: 0.496 AC XY: 36824 AN XY: 74184

Gnomad4 AFR AF: 0.307

Gnomad4 AMR AF: 0.483

Gnomad4 ASJ AF: 0.627

Gnomad4 EAS AF: 0.379

Gnomad4 SAS AF: 0.612

Gnomad4 FIN AF: 0.583

Gnomad4 NFE AF: 0.591

Gnomad4 OTH AF: 0.513

Alfa AF: 0.566 Hom.: 11889

Bravo AF: 0.473

Asia WGS AF: 0.437 AC: 1518 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	0.85
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1454909; hg19: chr5-57252398;