rs27323

Variant names:

• chr5-53256409-G-A
• rs27323

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 0.574 in 151,968 control chromosomes in the GnomAD database, including 25,282 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 0.57 (25282 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.830

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) 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: 0.574 AC: 87151 AN: 151850 Hom.: 25272 Cov.: 32

Gnomad AFR AF: 0.560

Gnomad AMI AF: 0.674

Gnomad AMR AF: 0.575

Gnomad ASJ AF: 0.548

Gnomad EAS AF: 0.426

Gnomad SAS AF: 0.417

Gnomad FIN AF: 0.605

Gnomad MID AF: 0.579

Gnomad NFE AF: 0.599

Gnomad OTH AF: 0.591

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

GnomAD4 genome AF: 0.574 AC: 87196 AN: 151968 Hom.: 25282 Cov.: 32 AF XY: 0.568 AC XY: 42186 AN XY: 74272

Gnomad4 AFR AF: 0.559

Gnomad4 AMR AF: 0.575

Gnomad4 ASJ AF: 0.548

Gnomad4 EAS AF: 0.427

Gnomad4 SAS AF: 0.417

Gnomad4 FIN AF: 0.605

Gnomad4 NFE AF: 0.599

Gnomad4 OTH AF: 0.588

Alfa AF: 0.592 Hom.: 35134

Bravo AF: 0.579

Asia WGS AF: 0.423 AC: 1473 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	9.9
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs27323; hg19: chr5-52552239;