rs1454909

chr5-57956571-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 0.495 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/exons	MANE	UniProt

Ensembl

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