ENST00000786276.1:n.194-47585T>C

Variant names:

• chr9-80873949-T-C
• rs11138885
• ENST00000786276.1:n.194-47585T>C

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000786276.1(ENSG00000302378):​n.194-47585T>C variant causes a intron change. The variant allele was found at a frequency of 0.152 in 151,972 control chromosomes in the GnomAD database, including 2,193 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 0.15 (2193 hom., cov: 32)
• Consequence: ENSG00000302378 ENST00000786276.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.92
• Publications: 4 publications found

Genes affected

ENSG00000302378 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.33).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.308 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

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
	ENSG00000302378	ENST00000786276.1		n.194-47585T>C		intron	N/A
	ENSG00000226798	ENST00000786374.1		n.211-2655A>G		intron	N/A
	ENSG00000226798	ENST00000786375.1		n.387-2655A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.152 AC: 23060 AN: 151854 Hom.: 2186 Cov.: 32

Gnomad AFR AF: 0.204

Gnomad AMI AF: 0.0901

Gnomad AMR AF: 0.243

Gnomad ASJ AF: 0.110

Gnomad EAS AF: 0.320

Gnomad SAS AF: 0.182

Gnomad FIN AF: 0.175

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.0834

Gnomad OTH AF: 0.174

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

GnomAD4 genome AF: 0.152 AC: 23086 AN: 151972 Hom.: 2193 Cov.: 32 AF XY: 0.160 AC XY: 11899 AN XY: 74292

African (AFR) AF: 0.204 AC: 8454 AN: 41496

American (AMR) AF: 0.243 AC: 3709 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.110 AC: 380 AN: 3466

East Asian (EAS) AF: 0.321 AC: 1657 AN: 5168

South Asian (SAS) AF: 0.181 AC: 875 AN: 4828

European-Finnish (FIN) AF: 0.175 AC: 1850 AN: 10582

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.0835 AC: 5665 AN: 67884

Other (OTH) AF: 0.174 AC: 365 AN: 2100

Alfa AF: 0.106 Hom.: 4854

Bravo AF: 0.159

Asia WGS AF: 0.232 AC: 806 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.33
CADD	Benign	17
DANN	Benign	0.87
PhyloP100		4.9

Splicing

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

Other links and lift over

dbSNP: rs11138885; hg19: chr9-83488864;