rs27323

Variant names:

• chr5-53256409-G-A
• rs27323

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 0.574 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
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.559 AC: 23182 AN: 41454

American (AMR) AF: 0.575 AC: 8771 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.548 AC: 1900 AN: 3470

East Asian (EAS) AF: 0.427 AC: 2192 AN: 5136

South Asian (SAS) AF: 0.417 AC: 2009 AN: 4816

European-Finnish (FIN) AF: 0.605 AC: 6391 AN: 10562

Middle Eastern (MID) AF: 0.575 AC: 169 AN: 294

European-Non Finnish (NFE) AF: 0.599 AC: 40728 AN: 67964

Other (OTH) AF: 0.588 AC: 1241 AN: 2110

Alfa AF: 0.589 Hom.: 54939

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
PhyloP100		0.83

Splicing

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

Other links and lift over

dbSNP: rs27323; hg19: chr5-52552239;