rs9519026

chr13-103382363-C-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000648788.1(ENSG00000285789):n.56-9864C>G variant causes a intron, non coding transcript 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: ENST00000648788.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.305

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000648788.1	n.56-9864C>G		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.0105

Gnomad4 AMR AF: 0.0519

Gnomad4 ASJ AF: 0.0804

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.00890

Gnomad4 FIN AF: 0.0167

Gnomad4 NFE AF: 0.0583

Gnomad4 OTH AF: 0.0516

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	2.1
Dann	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9519026; hg19: chr13-104034713;