rs1927745

chr13-107127968-G-Achr13-107127968-G-C

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 0.268 in 151,972 control chromosomes in the GnomAD database, including 5,603 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 0.27 (5603 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.236

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.382 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.268 AC: 40694 AN: 151854 Hom.: 5607 Cov.: 32

Gnomad AFR AF: 0.311

Gnomad AMI AF: 0.110

Gnomad AMR AF: 0.210

Gnomad ASJ AF: 0.250

Gnomad EAS AF: 0.398

Gnomad SAS AF: 0.278

Gnomad FIN AF: 0.305

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.243

Gnomad OTH AF: 0.237

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

GnomAD4 genome AF: 0.268 AC: 40717 AN: 151972 Hom.: 5603 Cov.: 32 AF XY: 0.271 AC XY: 20092 AN XY: 74276

Gnomad4 AFR AF: 0.311

Gnomad4 AMR AF: 0.210

Gnomad4 ASJ AF: 0.250

Gnomad4 EAS AF: 0.396

Gnomad4 SAS AF: 0.278

Gnomad4 FIN AF: 0.305

Gnomad4 NFE AF: 0.243

Gnomad4 OTH AF: 0.238

Alfa AF: 0.244 Hom.: 9665

Bravo AF: 0.262

Asia WGS AF: 0.345 AC: 1199 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	2.2
Dann	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1927745; hg19: chr13-107780316;