rs10119177

Variant names:

• chr9-16212181-G-C
• rs10119177
• ENST00000380685.5:n.275+3035C>G

Your query was ambiguous. Multiple possible variants found:

• chr9-16212181-G-C
• chr9-16212181-G-T

Variant summary

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

The ENST00000380685.5(LINC03041):​n.275+3035C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.342 in 151,996 control chromosomes in the GnomAD database, including 10,091 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 0.34 (10091 hom., cov: 32)
• Consequence: LINC03041 ENST00000380685.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.91
• Publications: 3 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=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.603 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000380685.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC03041	NR_171034.1		n.275+3035C>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC03041	ENST00000380685.5	TSL:2	n.275+3035C>G		intron	N/A
	LINC03041	ENST00000433347.2	TSL:3	n.267+3035C>G		intron	N/A
	LINC03041	ENST00000648575.1		n.301+3591C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.342 AC: 51948 AN: 151878 Hom.: 10082 Cov.: 32

Gnomad AFR AF: 0.495

Gnomad AMI AF: 0.168

Gnomad AMR AF: 0.317

Gnomad ASJ AF: 0.293

Gnomad EAS AF: 0.621

Gnomad SAS AF: 0.438

Gnomad FIN AF: 0.324

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.236

Gnomad OTH AF: 0.308

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

GnomAD4 genome AF: 0.342 AC: 51991 AN: 151996 Hom.: 10091 Cov.: 32 AF XY: 0.348 AC XY: 25869 AN XY: 74270

African (AFR) AF: 0.495 AC: 20498 AN: 41422

American (AMR) AF: 0.317 AC: 4843 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.293 AC: 1015 AN: 3470

East Asian (EAS) AF: 0.621 AC: 3209 AN: 5164

South Asian (SAS) AF: 0.438 AC: 2104 AN: 4806

European-Finnish (FIN) AF: 0.324 AC: 3420 AN: 10560

Middle Eastern (MID) AF: 0.269 AC: 79 AN: 294

European-Non Finnish (NFE) AF: 0.236 AC: 16023 AN: 67980

Other (OTH) AF: 0.307 AC: 647 AN: 2110

Alfa AF: 0.177 Hom.: 358

Bravo AF: 0.346

Asia WGS AF: 0.473 AC: 1644 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.63
DANN	Benign	0.30
PhyloP100		-1.9

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs10119177; hg19: chr9-16212179;