9-84099087-C-A

Variant names:

• chr9-84099087-C-A
• rs7032430
• ENST00000783238.1:n.935C>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000783238.1(ENSG00000227463):​n.935C>A variant causes a non coding transcript exon 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 ENST00000783238.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.62
• Publications: 2 publications found

Genes affected

ENSG00000227463 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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	ENST00000783238.1	n.935C>A		non_coding_transcript_exon_variant	Exon 3 of 3
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

African (AFR) AF: 0.223 AC: 9220 AN: 41394

American (AMR) AF: 0.309 AC: 4711 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.173 AC: 599 AN: 3472

East Asian (EAS) AF: 0.305 AC: 1572 AN: 5156

South Asian (SAS) AF: 0.213 AC: 1028 AN: 4822

European-Finnish (FIN) AF: 0.203 AC: 2136 AN: 10530

Middle Eastern (MID) AF: 0.211 AC: 62 AN: 294

European-Non Finnish (NFE) AF: 0.216 AC: 14652 AN: 67960

Other (OTH) AF: 0.240 AC: 505 AN: 2108

Alfa AF: 0.222 Hom.: 9899

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
PhyloP100		1.6

Splicing

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

Other links and lift over

dbSNP: rs7032430; hg19: chr9-86714002;