ENST00000778316.1:n.384+24676C>A

Variant names:

• chr9-21293632-C-A
• rs1360286
• ENST00000778316.1:n.384+24676C>A

Variant summary

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

The ENST00000778316.1(ENSG00000301340):​n.384+24676C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.248 in 151,692 control chromosomes in the GnomAD database, including 4,933 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 0.25 (4933 hom., cov: 30)
• Consequence: ENSG00000301340 ENST00000778316.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.41
• Publications: 10 publications found

Genes affected

ENSG00000301340 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.455 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000778316.1. 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
	ENSG00000301340	ENST00000778316.1		n.384+24676C>A		intron	N/A
	ENSG00000301340	ENST00000778317.1		n.538+24676C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.248 AC: 37620 AN: 151572 Hom.: 4925 Cov.: 30

Gnomad AFR AF: 0.284

Gnomad AMI AF: 0.166

Gnomad AMR AF: 0.298

Gnomad ASJ AF: 0.239

Gnomad EAS AF: 0.471

Gnomad SAS AF: 0.157

Gnomad FIN AF: 0.211

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.213

Gnomad OTH AF: 0.246

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

GnomAD4 genome AF: 0.248 AC: 37675 AN: 151692 Hom.: 4933 Cov.: 30 AF XY: 0.248 AC XY: 18408 AN XY: 74104

African (AFR) AF: 0.284 AC: 11762 AN: 41380

American (AMR) AF: 0.298 AC: 4544 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.239 AC: 828 AN: 3466

East Asian (EAS) AF: 0.471 AC: 2389 AN: 5076

South Asian (SAS) AF: 0.159 AC: 764 AN: 4800

European-Finnish (FIN) AF: 0.211 AC: 2230 AN: 10544

Middle Eastern (MID) AF: 0.224 AC: 66 AN: 294

European-Non Finnish (NFE) AF: 0.213 AC: 14425 AN: 67878

Other (OTH) AF: 0.245 AC: 516 AN: 2102

Alfa AF: 0.224 Hom.: 3463

Bravo AF: 0.260

Asia WGS AF: 0.307 AC: 1067 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.3
DANN	Benign	0.32
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs1360286; hg19: chr9-21293631;