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. The variant received -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
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.323 AC: 13400 AN: 41450

American (AMR) AF: 0.164 AC: 2508 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.210 AC: 729 AN: 3466

East Asian (EAS) AF: 0.165 AC: 853 AN: 5180

South Asian (SAS) AF: 0.259 AC: 1246 AN: 4820

European-Finnish (FIN) AF: 0.202 AC: 2142 AN: 10586

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.197 AC: 13391 AN: 67974

Other (OTH) AF: 0.217 AC: 457 AN: 2104

Alfa AF: 0.209 Hom.: 10692

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
PhyloP100		-0.75

Splicing

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

Other links and lift over

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