17-81379355-T-C

Variant summary

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

The NR_164137.1(LINC03048):n.514+367A>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 0.653 in 151,968 control chromosomes in the GnomAD database, including 32,703 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 0.65 (32703 hom., cov: 32)
• Consequence: LINC03048 NR_164137.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.97

Genes affected

LINC03048 (HGNC:56272): (long intergenic non-protein coding RNA 3048)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.83 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC03048	NR_164137.1	n.514+367A>G		intron_variant, non_coding_transcript_variant
LINC03048	NR_164138.1	n.440+367A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC03048	ENST00000648736.1	n.543+367A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.653 AC: 99157 AN: 151852 Hom.: 32687 Cov.: 32

Gnomad AFR AF: 0.597

Gnomad AMI AF: 0.686

Gnomad AMR AF: 0.730

Gnomad ASJ AF: 0.728

Gnomad EAS AF: 0.851

Gnomad SAS AF: 0.633

Gnomad FIN AF: 0.615

Gnomad MID AF: 0.688

Gnomad NFE AF: 0.657

Gnomad OTH AF: 0.673

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

GnomAD4 genome AF: 0.653 AC: 99212 AN: 151968 Hom.: 32703 Cov.: 32 AF XY: 0.657 AC XY: 48757 AN XY: 74260

Gnomad4 AFR AF: 0.596

Gnomad4 AMR AF: 0.730

Gnomad4 ASJ AF: 0.728

Gnomad4 EAS AF: 0.851

Gnomad4 SAS AF: 0.634

Gnomad4 FIN AF: 0.615

Gnomad4 NFE AF: 0.657

Gnomad4 OTH AF: 0.666

Alfa AF: 0.588 Hom.: 2646

Bravo AF: 0.666

Asia WGS AF: 0.631 AC: 2198 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	0.13
Dann	Benign	0.15

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11651296; hg19: chr17-79353155;