rs7873766

Variant names:

• chr9-32290483-T-C
• rs7873766
• ENST00000784938.1:n.705-7978A>G

Variant summary

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

The ENST00000784938.1(ENSG00000302201):​n.705-7978A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.119 in 152,190 control chromosomes in the GnomAD database, including 1,319 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 0.12 (1319 hom., cov: 32)
• Consequence: ENSG00000302201 ENST00000784938.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.283
• Publications: 3 publications found

Genes affected

ENSG00000302201 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.238 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000784938.1. 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
	ENSG00000302201	ENST00000784938.1		n.705-7978A>G		intron	N/A
	ENSG00000302201	ENST00000784939.1		n.395-7978A>G		intron	N/A
	ENSG00000302201	ENST00000784940.1		n.197-7978A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.119 AC: 18033 AN: 152072 Hom.: 1311 Cov.: 32

Gnomad AFR AF: 0.136

Gnomad AMI AF: 0.0967

Gnomad AMR AF: 0.207

Gnomad ASJ AF: 0.144

Gnomad EAS AF: 0.250

Gnomad SAS AF: 0.147

Gnomad FIN AF: 0.0154

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.0906

Gnomad OTH AF: 0.142

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

GnomAD4 genome AF: 0.119 AC: 18056 AN: 152190 Hom.: 1319 Cov.: 32 AF XY: 0.119 AC XY: 8843 AN XY: 74414

African (AFR) AF: 0.136 AC: 5647 AN: 41518

American (AMR) AF: 0.207 AC: 3166 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.144 AC: 499 AN: 3472

East Asian (EAS) AF: 0.250 AC: 1289 AN: 5160

South Asian (SAS) AF: 0.147 AC: 705 AN: 4810

European-Finnish (FIN) AF: 0.0154 AC: 163 AN: 10616

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.0906 AC: 6161 AN: 68010

Other (OTH) AF: 0.149 AC: 314 AN: 2112

Alfa AF: 0.108 Hom.: 195

Bravo AF: 0.134

Asia WGS AF: 0.198 AC: 688 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	5.1
DANN	Benign	0.84
PhyloP100		0.28

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: rs7873766;

hg19: chr9-32290481;