rs9406636

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr9-16385134-C-A
• chr9-16385134-C-T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.617 AC: 25550 AN: 41442

American (AMR) AF: 0.668 AC: 10201 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.693 AC: 2405 AN: 3468

East Asian (EAS) AF: 0.580 AC: 2989 AN: 5154

South Asian (SAS) AF: 0.643 AC: 3102 AN: 4826

European-Finnish (FIN) AF: 0.591 AC: 6236 AN: 10552

Middle Eastern (MID) AF: 0.646 AC: 190 AN: 294

European-Non Finnish (NFE) AF: 0.601 AC: 40793 AN: 67930

Other (OTH) AF: 0.591 AC: 1248 AN: 2112

Alfa AF: 0.580 Hom.: 6156

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
PhyloP100		-0.84

Splicing

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

Other links and lift over

dbSNP: rs9406636; hg19: chr9-16385132;