rs9568087

chr13-48713188-T-Achr13-48713188-T-Cchr13-48713188-T-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 0.236 in 152,162 control chromosomes in the GnomAD database, including 5,241 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 0.24 (5241 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.66

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.427 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: 0.236 AC: 35876 AN: 152044 Hom.: 5244 Cov.: 32

Gnomad AFR AF: 0.0620

Gnomad AMI AF: 0.329

Gnomad AMR AF: 0.257

Gnomad ASJ AF: 0.260

Gnomad EAS AF: 0.442

Gnomad SAS AF: 0.384

Gnomad FIN AF: 0.350

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.291

Gnomad OTH AF: 0.233

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

GnomAD4 genome AF: 0.236 AC: 35872 AN: 152162 Hom.: 5241 Cov.: 32 AF XY: 0.244 AC XY: 18160 AN XY: 74382

Gnomad4 AFR AF: 0.0620

Gnomad4 AMR AF: 0.258

Gnomad4 ASJ AF: 0.260

Gnomad4 EAS AF: 0.442

Gnomad4 SAS AF: 0.383

Gnomad4 FIN AF: 0.350

Gnomad4 NFE AF: 0.291

Gnomad4 OTH AF: 0.231

Alfa AF: 0.264 Hom.: 732

Bravo AF: 0.222

Asia WGS AF: 0.337 AC: 1174 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.24
Dann	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9568087; hg19: chr13-49287324;