rs27438

Variant names:

• chr5-132077562-G-A
• rs27438

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 0.343 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
• Publications: 16 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.576 AC: 23887 AN: 41458

American (AMR) AF: 0.249 AC: 3813 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.291 AC: 1008 AN: 3468

East Asian (EAS) AF: 0.616 AC: 3184 AN: 5172

South Asian (SAS) AF: 0.265 AC: 1275 AN: 4814

European-Finnish (FIN) AF: 0.350 AC: 3702 AN: 10566

Middle Eastern (MID) AF: 0.272 AC: 80 AN: 294

European-Non Finnish (NFE) AF: 0.213 AC: 14475 AN: 67988

Other (OTH) AF: 0.309 AC: 654 AN: 2114

Alfa AF: 0.254 Hom.: 7610

Bravo AF: 0.350

Asia WGS AF: 0.467 AC: 1627 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.40
DANN	Benign	0.61
PhyloP100		-0.61

Splicing

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

Other links and lift over

dbSNP: rs27438; hg19: chr5-131413255;