rs1888952

chr9-16258120-A-Gchr9-16258120-A-T

Variant summary

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

The NR_171034.1(LINC03041):n.83+18111T>C 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 0.488 in 152,054 control chromosomes in the GnomAD database, including 20,741 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 0.49 (20741 hom., cov: 32)
• Consequence: LINC03041 NR_171034.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.368

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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.914 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC03041	NR_171034.1	n.83+18111T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC03041	ENST00000648575.1	n.174-42221T>C		intron_variant, non_coding_transcript_variant
LINC03041	ENST00000380685.5	n.83+18111T>C		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.488 AC: 74180 AN: 151936 Hom.: 20743 Cov.: 32

Gnomad AFR AF: 0.209

Gnomad AMI AF: 0.346

Gnomad AMR AF: 0.602

Gnomad ASJ AF: 0.593

Gnomad EAS AF: 0.936

Gnomad SAS AF: 0.614

Gnomad FIN AF: 0.605

Gnomad MID AF: 0.583

Gnomad NFE AF: 0.566

Gnomad OTH AF: 0.535

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

GnomAD4 genome AF: 0.488 AC: 74190 AN: 152054 Hom.: 20741 Cov.: 32 AF XY: 0.499 AC XY: 37067 AN XY: 74310

Gnomad4 AFR AF: 0.209

Gnomad4 AMR AF: 0.603

Gnomad4 ASJ AF: 0.593

Gnomad4 EAS AF: 0.936

Gnomad4 SAS AF: 0.612

Gnomad4 FIN AF: 0.605

Gnomad4 NFE AF: 0.566

Gnomad4 OTH AF: 0.536

Alfa AF: 0.556 Hom.: 31005

Bravo AF: 0.478

Asia WGS AF: 0.705 AC: 2450 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	0.68
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: rs1888952; hg19: chr9-16258118; COSMIC: COSV66227367;