rs9285076

chr13-30769786-G-Achr13-30769786-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 0.23 in 152,082 control chromosomes in the GnomAD database, including 4,279 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 0.23 (4279 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.746

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.319 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: 0.230 AC: 34946 AN: 151964 Hom.: 4279 Cov.: 32

Gnomad AFR AF: 0.324

Gnomad AMI AF: 0.170

Gnomad AMR AF: 0.164

Gnomad ASJ AF: 0.210

Gnomad EAS AF: 0.164

Gnomad SAS AF: 0.258

Gnomad FIN AF: 0.202

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.197

Gnomad OTH AF: 0.217

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

GnomAD4 genome AF: 0.230 AC: 34954 AN: 152082 Hom.: 4279 Cov.: 32 AF XY: 0.227 AC XY: 16882 AN XY: 74346

Gnomad4 AFR AF: 0.323

Gnomad4 AMR AF: 0.164

Gnomad4 ASJ AF: 0.210

Gnomad4 EAS AF: 0.165

Gnomad4 SAS AF: 0.259

Gnomad4 FIN AF: 0.202

Gnomad4 NFE AF: 0.197

Gnomad4 OTH AF: 0.217

Alfa AF: 0.206 Hom.: 4558

Bravo AF: 0.229

Asia WGS AF: 0.212 AC: 741 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	1.6
Dann	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9285076; hg19: chr13-31343923; COSMIC: COSV65543443;