9-80911728-C-T

Variant names:

• chr9-80911728-C-T
• rs2209263
• ENST00000786276.1:n.194-9806C>T

Variant summary

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

The ENST00000786276.1(ENSG00000302378):​n.194-9806C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.224 in 151,372 control chromosomes in the GnomAD database, including 4,085 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 (4085 hom., cov: 31)
• Consequence: ENSG00000302378 ENST00000786276.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.673
• Publications: 1 publications found

Genes affected

ENSG00000302378 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.263 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000786276.1. 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
	ENSG00000302378	ENST00000786276.1		n.194-9806C>T		intron	N/A
	ENSG00000226798	ENST00000786374.1		n.79+10889G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.224 AC: 33906 AN: 151250 Hom.: 4081 Cov.: 31

Gnomad AFR AF: 0.154

Gnomad AMI AF: 0.343

Gnomad AMR AF: 0.210

Gnomad ASJ AF: 0.178

Gnomad EAS AF: 0.151

Gnomad SAS AF: 0.206

Gnomad FIN AF: 0.299

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.266

Gnomad OTH AF: 0.202

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

GnomAD4 genome AF: 0.224 AC: 33930 AN: 151372 Hom.: 4085 Cov.: 31 AF XY: 0.224 AC XY: 16554 AN XY: 73956

African (AFR) AF: 0.154 AC: 6368 AN: 41338

American (AMR) AF: 0.210 AC: 3179 AN: 15140

Ashkenazi Jewish (ASJ) AF: 0.178 AC: 616 AN: 3458

East Asian (EAS) AF: 0.151 AC: 778 AN: 5136

South Asian (SAS) AF: 0.208 AC: 997 AN: 4798

European-Finnish (FIN) AF: 0.299 AC: 3141 AN: 10490

Middle Eastern (MID) AF: 0.274 AC: 80 AN: 292

European-Non Finnish (NFE) AF: 0.266 AC: 18038 AN: 67716

Other (OTH) AF: 0.202 AC: 424 AN: 2102

Alfa AF: 0.243 Hom.: 9691

Bravo AF: 0.213

Asia WGS AF: 0.173 AC: 601 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.58
DANN	Benign	0.56
PhyloP100		-0.67

Splicing

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

Other links and lift over

dbSNP: rs2209263; hg19: chr9-83526643; COSMIC: COSV63297945;