rs27348

Variant names:

• chr5-132071446-T-A
• rs27348

Your query was ambiguous. Multiple possible variants found:

• chr5-132071446-T-A
• chr5-132071446-T-C
• chr5-132071446-T-G

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 0.239 in 151,790 control chromosomes in the GnomAD database, including 4,580 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 0.24 (4580 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.219
• Publications: 8 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.43 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: 0.239 AC: 36199 AN: 151672 Hom.: 4568 Cov.: 31

Gnomad AFR AF: 0.229

Gnomad AMI AF: 0.136

Gnomad AMR AF: 0.212

Gnomad ASJ AF: 0.272

Gnomad EAS AF: 0.445

Gnomad SAS AF: 0.229

Gnomad FIN AF: 0.381

Gnomad MID AF: 0.156

Gnomad NFE AF: 0.214

Gnomad OTH AF: 0.224

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

GnomAD4 genome AF: 0.239 AC: 36237 AN: 151790 Hom.: 4580 Cov.: 31 AF XY: 0.245 AC XY: 18184 AN XY: 74162

African (AFR) AF: 0.229 AC: 9472 AN: 41372

American (AMR) AF: 0.212 AC: 3239 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.272 AC: 943 AN: 3466

East Asian (EAS) AF: 0.445 AC: 2289 AN: 5146

South Asian (SAS) AF: 0.229 AC: 1101 AN: 4802

European-Finnish (FIN) AF: 0.381 AC: 4009 AN: 10528

Middle Eastern (MID) AF: 0.161 AC: 47 AN: 292

European-Non Finnish (NFE) AF: 0.214 AC: 14525 AN: 67914

Other (OTH) AF: 0.231 AC: 488 AN: 2110

Alfa AF: 0.239 Hom.: 545

Bravo AF: 0.230

Asia WGS AF: 0.387 AC: 1345 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	3.1
DANN	Benign	0.63
PhyloP100		0.22

Splicing

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

Other links and lift over

dbSNP: rs27348; hg19: chr5-131407139;