chr13-107127968-G-A

Variant names:

• chr13-107127968-G-A
• rs1927745

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 0.268 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
• Publications: 9 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	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

African (AFR) AF: 0.311 AC: 12892 AN: 41434

American (AMR) AF: 0.210 AC: 3208 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.250 AC: 868 AN: 3470

East Asian (EAS) AF: 0.396 AC: 2037 AN: 5138

South Asian (SAS) AF: 0.278 AC: 1342 AN: 4822

European-Finnish (FIN) AF: 0.305 AC: 3221 AN: 10554

Middle Eastern (MID) AF: 0.197 AC: 58 AN: 294

European-Non Finnish (NFE) AF: 0.243 AC: 16489 AN: 67968

Other (OTH) AF: 0.238 AC: 502 AN: 2110

Alfa AF: 0.249 Hom.: 15289

Bravo AF: 0.262

Asia WGS AF: 0.345 AC: 1199 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.2
DANN	Benign	0.29
PhyloP100		0.24

Splicing

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

Other links and lift over

dbSNP: rs1927745; hg19: chr13-107780316;