9-16385134-C-A

Variant names:

• chr9-16385134-C-A
• rs9406636
• ENST00000648575.1:n.173+15286G>T

Variant summary

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

The ENST00000648575.1(LINC03041):​n.173+15286G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.612 in 151,948 control chromosomes in the GnomAD database, including 28,751 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 0.61 (28751 hom., cov: 32)
• Consequence: LINC03041 ENST00000648575.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.843

Genes affected

LINC03041 (HGNC:19054): (long intergenic non-protein coding RNA 3041)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.658 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC03041	ENST00000648575.1	n.173+15286G>T		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.612 AC: 92990 AN: 151830 Hom.: 28722 Cov.: 32

Gnomad AFR AF: 0.617

Gnomad AMI AF: 0.376

Gnomad AMR AF: 0.668

Gnomad ASJ AF: 0.693

Gnomad EAS AF: 0.580

Gnomad SAS AF: 0.644

Gnomad FIN AF: 0.591

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.601

Gnomad OTH AF: 0.592

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

GnomAD4 genome AF: 0.612 AC: 93056 AN: 151948 Hom.: 28751 Cov.: 32 AF XY: 0.614 AC XY: 45590 AN XY: 74254

Gnomad4 AFR AF: 0.617

Gnomad4 AMR AF: 0.668

Gnomad4 ASJ AF: 0.693

Gnomad4 EAS AF: 0.580

Gnomad4 SAS AF: 0.643

Gnomad4 FIN AF: 0.591

Gnomad4 NFE AF: 0.601

Gnomad4 OTH AF: 0.591

Alfa AF: 0.511 Hom.: 1570

Bravo AF: 0.617

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.87
DANN	Benign	0.25

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9406636; hg19: chr9-16385132;