17-81379355-T-C

Variant names:

• chr17-81379355-T-C
• rs11651296
• ENST00000574041.6:n.809A>G

Variant summary

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

The ENST00000574041.6(LINC03048):​n.809A>G variant causes a non coding transcript exon 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 ENST00000574041.6 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.97
• Publications: 3 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LINC03048	NR_164137.1	n.514+367A>G		intron_variant	Intron 3 of 3
LINC03048	NR_164138.1	n.440+367A>G		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC03048	ENST00000574041.6	n.809A>G		non_coding_transcript_exon_variant	Exon 4 of 4	5
LINC03048	ENST00000570301.7	n.580+367A>G		intron_variant	Intron 4 of 4	3
LINC03048	ENST00000570929.1	n.202+367A>G		intron_variant	Intron 1 of 1	2

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

African (AFR) AF: 0.596 AC: 24725 AN: 41466

American (AMR) AF: 0.730 AC: 11159 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.728 AC: 2529 AN: 3472

East Asian (EAS) AF: 0.851 AC: 4368 AN: 5132

South Asian (SAS) AF: 0.634 AC: 3055 AN: 4816

European-Finnish (FIN) AF: 0.615 AC: 6511 AN: 10588

Middle Eastern (MID) AF: 0.695 AC: 203 AN: 292

European-Non Finnish (NFE) AF: 0.657 AC: 44634 AN: 67898

Other (OTH) AF: 0.666 AC: 1404 AN: 2108

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
PhyloP100		-5.0

Splicing

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

Other links and lift over

dbSNP: rs11651296; hg19: chr17-79353155;