ENST00000648788.1:n.56-9864C>G

Variant names:

• chr13-103382363-C-G
• rs9519026
• ENST00000648788.1:n.56-9864C>G

Variant summary

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

The ENST00000648788.1(ENSG00000285789):​n.56-9864C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.039 in 152,330 control chromosomes in the GnomAD database, including 173 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 0.039 (173 hom., cov: 33)
• Consequence: ENSG00000285789 ENST00000648788.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.305
• Publications: 2 publications found

Genes affected

ENSG00000285789 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0567 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000648788.1. 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
	ENSG00000285789	ENST00000648788.1		n.56-9864C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0390 AC: 5938 AN: 152212 Hom.: 173 Cov.: 33

Gnomad AFR AF: 0.0105

Gnomad AMI AF: 0.129

Gnomad AMR AF: 0.0520

Gnomad ASJ AF: 0.0804

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.00868

Gnomad FIN AF: 0.0167

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0583

Gnomad OTH AF: 0.0526

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

GnomAD4 genome AF: 0.0390 AC: 5936 AN: 152330 Hom.: 173 Cov.: 33 AF XY: 0.0359 AC XY: 2673 AN XY: 74496

African (AFR) AF: 0.0105 AC: 435 AN: 41588

American (AMR) AF: 0.0519 AC: 793 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0804 AC: 279 AN: 3472

East Asian (EAS) AF: 0.000386 AC: 2 AN: 5188

South Asian (SAS) AF: 0.00890 AC: 43 AN: 4832

European-Finnish (FIN) AF: 0.0167 AC: 177 AN: 10620

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.0583 AC: 3963 AN: 68018

Other (OTH) AF: 0.0516 AC: 109 AN: 2112

Alfa AF: 0.0470 Hom.: 33

Bravo AF: 0.0413

Asia WGS AF: 0.00837 AC: 29 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.1
DANN	Benign	0.47
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs9519026; hg19: chr13-104034713;