rs4961688

Positions:

• chr9-16262193-G-C
• chr9-16262193-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.83+14038C>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 0.52 in 152,128 control chromosomes in the GnomAD database, including 23,253 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 0.52 (23253 hom., cov: 33)
• Consequence: LINC03041 NR_171034.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.126

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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.922 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC03041	NR_171034.1	n.83+14038C>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC03041	ENST00000648575.1	n.174-46294C>G		intron_variant, non_coding_transcript_variant
LINC03041	ENST00000380685.5	n.83+14038C>G		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.520 AC: 79082 AN: 152012 Hom.: 23256 Cov.: 33

Gnomad AFR AF: 0.231

Gnomad AMI AF: 0.479

Gnomad AMR AF: 0.619

Gnomad ASJ AF: 0.584

Gnomad EAS AF: 0.944

Gnomad SAS AF: 0.629

Gnomad FIN AF: 0.668

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.607

Gnomad OTH AF: 0.561

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

GnomAD4 genome AF: 0.520 AC: 79092 AN: 152128 Hom.: 23253 Cov.: 33 AF XY: 0.531 AC XY: 39511 AN XY: 74368

Gnomad4 AFR AF: 0.231

Gnomad4 AMR AF: 0.619

Gnomad4 ASJ AF: 0.584

Gnomad4 EAS AF: 0.944

Gnomad4 SAS AF: 0.627

Gnomad4 FIN AF: 0.668

Gnomad4 NFE AF: 0.607

Gnomad4 OTH AF: 0.562

Alfa AF: 0.448 Hom.: 1452

Bravo AF: 0.505

Asia WGS AF: 0.725 AC: 2522 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.3
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4961688; hg19: chr9-16262191;