rs11651296

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr17-81379355-T-A
• chr17-81379355-T-C

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000574041.6(LINC03048):​n.809A>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC03048	NR_164137.1	n.514+367A>T		intron_variant	Intron 3 of 3
LINC03048	NR_164138.1	n.440+367A>T		intron_variant	Intron 3 of 3

Ensembl

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

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 2646

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.11
DANN	Benign	0.17
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;