rs256481

Variant names:

• chr5-5721950-C-T
• rs256481

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 0.533 in 151,850 control chromosomes in the GnomAD database, including 22,059 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 0.53 (22059 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.864

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.571 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: 0.533 AC: 80944 AN: 151732 Hom.: 22050 Cov.: 31

Gnomad AFR AF: 0.577

Gnomad AMI AF: 0.450

Gnomad AMR AF: 0.456

Gnomad ASJ AF: 0.522

Gnomad EAS AF: 0.221

Gnomad SAS AF: 0.522

Gnomad FIN AF: 0.563

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.545

Gnomad OTH AF: 0.546

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

GnomAD4 genome AF: 0.533 AC: 80983 AN: 151850 Hom.: 22059 Cov.: 31 AF XY: 0.529 AC XY: 39248 AN XY: 74182

Gnomad4 AFR AF: 0.577

Gnomad4 AMR AF: 0.455

Gnomad4 ASJ AF: 0.522

Gnomad4 EAS AF: 0.221

Gnomad4 SAS AF: 0.519

Gnomad4 FIN AF: 0.563

Gnomad4 NFE AF: 0.545

Gnomad4 OTH AF: 0.545

Alfa AF: 0.541 Hom.: 11873

Bravo AF: 0.527

Asia WGS AF: 0.391 AC: 1357 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.37
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs256481; hg19: chr5-5722063;