13-27270556-A-G

Position:

• chr13-27270556-A-G

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 0.455 in 199,084 control chromosomes in the GnomAD database, including 22,182 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 0.47 (18085 hom., cov: 33)
  • Exomes 𝑓: 0.40 (4097 hom.)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.138

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.631 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.471 AC: 71647 AN: 151988 Hom.: 18041 Cov.: 33

Gnomad AFR AF: 0.638

Gnomad AMI AF: 0.232

Gnomad AMR AF: 0.534

Gnomad ASJ AF: 0.352

Gnomad EAS AF: 0.603

Gnomad SAS AF: 0.345

Gnomad FIN AF: 0.479

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.363

Gnomad OTH AF: 0.475

GnomAD4 exome AF: 0.402 AC: 18904 AN: 46976 Hom.: 4097 Cov.: 0 AF XY: 0.402 AC XY: 9539 AN XY: 23748

Gnomad4 AFR exome AF: 0.628

Gnomad4 AMR exome AF: 0.572

Gnomad4 ASJ exome AF: 0.355

Gnomad4 EAS exome AF: 0.608

Gnomad4 SAS exome AF: 0.393

Gnomad4 FIN exome AF: 0.511

Gnomad4 NFE exome AF: 0.371

Gnomad4 OTH exome AF: 0.431

GnomAD4 genome AF: 0.472 AC: 71742 AN: 152108 Hom.: 18085 Cov.: 33 AF XY: 0.477 AC XY: 35449 AN XY: 74358

Gnomad4 AFR AF: 0.638

Gnomad4 AMR AF: 0.534

Gnomad4 ASJ AF: 0.352

Gnomad4 EAS AF: 0.603

Gnomad4 SAS AF: 0.345

Gnomad4 FIN AF: 0.479

Gnomad4 NFE AF: 0.363

Gnomad4 OTH AF: 0.471

Alfa AF: 0.371 Hom.: 14631

Bravo AF: 0.485

Asia WGS AF: 0.512 AC: 1783 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	6.4
DANN	Benign	0.66

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs7331765; hg19: chr13-27844693;