rs9285076

Variant names:

• chr13-30769786-G-A
• rs9285076

Your query was ambiguous. Multiple possible variants found:

• chr13-30769786-G-A
• chr13-30769786-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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;