rs1888952

Variant names:

• chr9-16258120-A-G
• rs1888952
• ENST00000380685.5:n.83+18111T>C

Your query was ambiguous. Multiple possible variants found:

• chr9-16258120-A-G
• chr9-16258120-A-T

Variant summary

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

The ENST00000380685.5(LINC03041):​n.83+18111T>C variant causes a intron 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 ENST00000380685.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.368
• Publications: 8 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=-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 rank	MANE	Protein	UniProt
LINC03041	NR_171034.1	n.83+18111T>C		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC03041	ENST00000380685.5	n.83+18111T>C		intron_variant	Intron 1 of 3	2
LINC03041	ENST00000648575.1	n.174-42221T>C		intron_variant	Intron 2 of 3

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

African (AFR) AF: 0.209 AC: 8669 AN: 41508

American (AMR) AF: 0.603 AC: 9205 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.593 AC: 2057 AN: 3470

East Asian (EAS) AF: 0.936 AC: 4833 AN: 5162

South Asian (SAS) AF: 0.612 AC: 2945 AN: 4814

European-Finnish (FIN) AF: 0.605 AC: 6391 AN: 10566

Middle Eastern (MID) AF: 0.586 AC: 171 AN: 292

European-Non Finnish (NFE) AF: 0.566 AC: 38473 AN: 67944

Other (OTH) AF: 0.536 AC: 1130 AN: 2108

Alfa AF: 0.545 Hom.: 38523

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
PhyloP100		-0.37

Splicing

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

Other links and lift over

dbSNP: rs1888952; hg19: chr9-16258118; COSMIC: COSV66227367;