rs27438

Variant names:

• chr5-132077562-G-A
• rs27438

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 0.343 in 152,070 control chromosomes in the GnomAD database, including 11,056 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 0.34 (11056 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.606

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.598 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: 0.343 AC: 52147 AN: 151952 Hom.: 11032 Cov.: 32

Gnomad AFR AF: 0.576

Gnomad AMI AF: 0.158

Gnomad AMR AF: 0.250

Gnomad ASJ AF: 0.291

Gnomad EAS AF: 0.616

Gnomad SAS AF: 0.265

Gnomad FIN AF: 0.350

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.213

Gnomad OTH AF: 0.302

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

GnomAD4 genome AF: 0.343 AC: 52222 AN: 152070 Hom.: 11056 Cov.: 32 AF XY: 0.348 AC XY: 25855 AN XY: 74330

Gnomad4 AFR AF: 0.576

Gnomad4 AMR AF: 0.249

Gnomad4 ASJ AF: 0.291

Gnomad4 EAS AF: 0.616

Gnomad4 SAS AF: 0.265

Gnomad4 FIN AF: 0.350

Gnomad4 NFE AF: 0.213

Gnomad4 OTH AF: 0.309

Alfa AF: 0.240 Hom.: 5089

Bravo AF: 0.350

Asia WGS AF: 0.467 AC: 1627 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.40
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs27438; hg19: chr5-131413255;