rs27437

Variant names:

• chr5-132101268-A-G
• rs27437

Your query was ambiguous. Multiple possible variants found:

• chr5-132101268-A-G
• chr5-132101268-A-T

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 0.396 in 151,926 control chromosomes in the GnomAD database, including 12,551 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 0.40 (12551 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.807
• Publications: 14 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 (AMR) allele frequency at 95% confidence interval = 0.481 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: 0.396 AC: 60142 AN: 151808 Hom.: 12547 Cov.: 32

Gnomad AFR AF: 0.293

Gnomad AMI AF: 0.621

Gnomad AMR AF: 0.490

Gnomad ASJ AF: 0.367

Gnomad EAS AF: 0.262

Gnomad SAS AF: 0.151

Gnomad FIN AF: 0.405

Gnomad MID AF: 0.306

Gnomad NFE AF: 0.462

Gnomad OTH AF: 0.435

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

GnomAD4 genome AF: 0.396 AC: 60165 AN: 151926 Hom.: 12551 Cov.: 32 AF XY: 0.388 AC XY: 28797 AN XY: 74240

African (AFR) AF: 0.293 AC: 12151 AN: 41424

American (AMR) AF: 0.490 AC: 7489 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.367 AC: 1272 AN: 3470

East Asian (EAS) AF: 0.262 AC: 1355 AN: 5164

South Asian (SAS) AF: 0.150 AC: 723 AN: 4812

European-Finnish (FIN) AF: 0.405 AC: 4261 AN: 10534

Middle Eastern (MID) AF: 0.312 AC: 91 AN: 292

European-Non Finnish (NFE) AF: 0.462 AC: 31354 AN: 67932

Other (OTH) AF: 0.430 AC: 908 AN: 2112

Alfa AF: 0.446 Hom.: 7257

Bravo AF: 0.409

Asia WGS AF: 0.219 AC: 764 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	6.1
DANN	Benign	0.48
PhyloP100		0.81

Splicing

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

Other links and lift over

dbSNP: rs27437; hg19: chr5-131436961; COSMIC: COSV60199042;