rs7032430

Variant names:

• chr9-84099087-C-A
• rs7032430
• ENST00000658503.1:n.*103C>A

Your query was ambiguous. Multiple possible variants found:

• chr9-84099087-C-A
• chr9-84099087-C-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000658503.1(ENSG00000227463):​n.*103C>A variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.228 in 151,898 control chromosomes in the GnomAD database, including 3,999 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 (3999 hom., cov: 33)
• Consequence: ENSG00000227463 ENST00000658503.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.62

Genes affected

ENSG00000227463 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.5).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.301 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
ENSG00000227463	ENST00000658503.1	n.*103C>A		downstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.228 AC: 34653 AN: 151780 Hom.: 3995 Cov.: 33

Gnomad AFR AF: 0.223

Gnomad AMI AF: 0.222

Gnomad AMR AF: 0.309

Gnomad ASJ AF: 0.173

Gnomad EAS AF: 0.306

Gnomad SAS AF: 0.214

Gnomad FIN AF: 0.203

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.216

Gnomad OTH AF: 0.241

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

GnomAD4 genome AF: 0.228 AC: 34686 AN: 151898 Hom.: 3999 Cov.: 33 AF XY: 0.230 AC XY: 17065 AN XY: 74228

Gnomad4 AFR AF: 0.223

Gnomad4 AMR AF: 0.309

Gnomad4 ASJ AF: 0.173

Gnomad4 EAS AF: 0.305

Gnomad4 SAS AF: 0.213

Gnomad4 FIN AF: 0.203

Gnomad4 NFE AF: 0.216

Gnomad4 OTH AF: 0.240

Alfa AF: 0.222 Hom.: 3705

Bravo AF: 0.237

Asia WGS AF: 0.247 AC: 863 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.50
CADD	Benign	15
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7032430; hg19: chr9-86714002;