rs1927745

Variant names:

• chr13-107127968-G-A
• rs1927745

Your query was ambiguous. Multiple possible variants found:

• chr13-107127968-G-A
• chr13-107127968-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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;