rs10119177

Positions:

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

Variant summary

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

The NR_171034.1(LINC03041):​n.275+3035C>G 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 0.342 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 NR_171034.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.91

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=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.603 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC03041	NR_171034.1	n.275+3035C>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC03041	ENST00000648575.1	n.301+3591C>G		intron_variant, non_coding_transcript_variant
LINC03041	ENST00000380685.5	n.275+3035C>G		intron_variant, non_coding_transcript_variant		2
LINC03041	ENST00000433347.2	n.267+3035C>G		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR AF: 0.495

Gnomad4 AMR AF: 0.317

Gnomad4 ASJ AF: 0.293

Gnomad4 EAS AF: 0.621

Gnomad4 SAS AF: 0.438

Gnomad4 FIN AF: 0.324

Gnomad4 NFE AF: 0.236

Gnomad4 OTH AF: 0.307

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 v4.3

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

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

Publications

LitVar

Other links and lift over

dbSNP: rs10119177; hg19: chr9-16212179;