6-29266733-C-G

Variant summary

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

The NR_134630.1(LINC03003):n.80-23393C>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 0.0789 in 152,026 control chromosomes in the GnomAD database, including 533 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 0.079 (533 hom., cov: 32)
• Consequence: LINC03003 NR_134630.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.253

Genes affected

LINC03003 (HGNC:56126): (long intergenic non-protein coding RNA 3003)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.127 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC03003	NR_134630.1	n.80-23393C>G		intron_variant, non_coding_transcript_variant
LINC03003	NR_134629.1	n.310-198C>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC03003	ENST00000606648.1	n.53-23393C>G		intron_variant, non_coding_transcript_variant		3
LINC03003	ENST00000441381.1	n.310-198C>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.0790 AC: 12005 AN: 151908 Hom.: 534 Cov.: 32

Gnomad AFR AF: 0.0728

Gnomad AMI AF: 0.0669

Gnomad AMR AF: 0.0671

Gnomad ASJ AF: 0.157

Gnomad EAS AF: 0.0879

Gnomad SAS AF: 0.137

Gnomad FIN AF: 0.132

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0687

Gnomad OTH AF: 0.0820

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

GnomAD4 genome AF: 0.0789 AC: 11999 AN: 152026 Hom.: 533 Cov.: 32 AF XY: 0.0832 AC XY: 6185 AN XY: 74320

Gnomad4 AFR AF: 0.0727

Gnomad4 AMR AF: 0.0672

Gnomad4 ASJ AF: 0.157

Gnomad4 EAS AF: 0.0867

Gnomad4 SAS AF: 0.136

Gnomad4 FIN AF: 0.132

Gnomad4 NFE AF: 0.0687

Gnomad4 OTH AF: 0.0816

Alfa AF: 0.0422 Hom.: 42

Bravo AF: 0.0720

Asia WGS AF: 0.113 AC: 392 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	3.2
Dann	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10484545; hg19: chr6-29234510;