9-78370826-T-C

Variant names:

• chr9-78370826-T-C
• rs2989579
• ENST00000832999.1:n.44+12174T>C

Variant summary

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

The ENST00000832999.1(ENSG00000308288):​n.44+12174T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.219 in 152,206 control chromosomes in the GnomAD database, including 4,018 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 0.22 (4018 hom., cov: 33)
• Consequence: ENSG00000308288 ENST00000832999.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.36
• Publications: 7 publications found

Genes affected

ENSG00000308288 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.256 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000832999.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000308288	ENST00000832999.1		n.44+12174T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.219 AC: 33252 AN: 152088 Hom.: 4014 Cov.: 33

Gnomad AFR AF: 0.141

Gnomad AMI AF: 0.316

Gnomad AMR AF: 0.229

Gnomad ASJ AF: 0.280

Gnomad EAS AF: 0.0550

Gnomad SAS AF: 0.191

Gnomad FIN AF: 0.311

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.259

Gnomad OTH AF: 0.219

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

GnomAD4 genome AF: 0.219 AC: 33272 AN: 152206 Hom.: 4018 Cov.: 33 AF XY: 0.218 AC XY: 16235 AN XY: 74404

African (AFR) AF: 0.141 AC: 5847 AN: 41554

American (AMR) AF: 0.229 AC: 3495 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.280 AC: 973 AN: 3472

East Asian (EAS) AF: 0.0551 AC: 286 AN: 5186

South Asian (SAS) AF: 0.192 AC: 927 AN: 4828

European-Finnish (FIN) AF: 0.311 AC: 3285 AN: 10564

Middle Eastern (MID) AF: 0.313 AC: 92 AN: 294

European-Non Finnish (NFE) AF: 0.259 AC: 17622 AN: 68004

Other (OTH) AF: 0.216 AC: 457 AN: 2114

Alfa AF: 0.231 Hom.: 3741

Bravo AF: 0.211

Asia WGS AF: 0.116 AC: 403 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.5
DANN	Benign	0.47
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs2989579; hg19: chr9-80985742; COSMIC: COSV60363064;