rs7030233

Variant names:

• chr9-132375086-A-G
• rs7030233
• ENST00000792639.1:n.516A>G

Variant summary

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

The ENST00000792639.1(ENSG00000303195):​n.516A>G 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 0.195 in 152,090 control chromosomes in the GnomAD database, including 3,000 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 0.19 (3000 hom., cov: 32)
• Consequence: ENSG00000303195 ENST00000792639.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.226
• Publications: 6 publications found

Genes affected

ENSG00000303195 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.303 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000792639.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000303195	ENST00000792639.1		n.516A>G		non_coding_transcript_exon	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.195 AC: 29614 AN: 151972 Hom.: 3001 Cov.: 32

Gnomad AFR AF: 0.214

Gnomad AMI AF: 0.162

Gnomad AMR AF: 0.191

Gnomad ASJ AF: 0.188

Gnomad EAS AF: 0.316

Gnomad SAS AF: 0.170

Gnomad FIN AF: 0.160

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.183

Gnomad OTH AF: 0.201

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

GnomAD4 genome AF: 0.195 AC: 29624 AN: 152090 Hom.: 3000 Cov.: 32 AF XY: 0.195 AC XY: 14464 AN XY: 74350

African (AFR) AF: 0.214 AC: 8861 AN: 41480

American (AMR) AF: 0.191 AC: 2910 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.188 AC: 653 AN: 3472

East Asian (EAS) AF: 0.316 AC: 1638 AN: 5182

South Asian (SAS) AF: 0.169 AC: 815 AN: 4816

European-Finnish (FIN) AF: 0.160 AC: 1691 AN: 10572

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.183 AC: 12432 AN: 67982

Other (OTH) AF: 0.197 AC: 416 AN: 2116

Alfa AF: 0.188 Hom.: 3367

Bravo AF: 0.199

Asia WGS AF: 0.234 AC: 816 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.3
DANN	Benign	0.81
PhyloP100		-0.23

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs7030233;

hg19: chr9-135250473;

COSMIC: COSV57502979;