6-134610162-A-G

Variant summary

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

The ENST00000655921.2(LINC03002):n.106-69539T>C 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 0.823 in 152,130 control chromosomes in the GnomAD database, including 51,844 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 0.82 (51844 hom., cov: 32)
• Consequence: LINC03002 ENST00000655921.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.71

Genes affected

LINC03002 (HGNC:56123): (long intergenic non-protein coding RNA 3002)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.975 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC03002	ENST00000655921.2	n.106-69539T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.823 AC: 125119 AN: 152012 Hom.: 51794 Cov.: 32

Gnomad AFR AF: 0.867

Gnomad AMI AF: 0.554

Gnomad AMR AF: 0.846

Gnomad ASJ AF: 0.737

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.770

Gnomad FIN AF: 0.812

Gnomad MID AF: 0.680

Gnomad NFE AF: 0.793

Gnomad OTH AF: 0.789

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

GnomAD4 genome AF: 0.823 AC: 125230 AN: 152130 Hom.: 51844 Cov.: 32 AF XY: 0.824 AC XY: 61302 AN XY: 74374

Gnomad4 AFR AF: 0.867

Gnomad4 AMR AF: 0.846

Gnomad4 ASJ AF: 0.737

Gnomad4 EAS AF: 0.998

Gnomad4 SAS AF: 0.769

Gnomad4 FIN AF: 0.812

Gnomad4 NFE AF: 0.793

Gnomad4 OTH AF: 0.791

Alfa AF: 0.792 Hom.: 19171

Bravo AF: 0.828

Asia WGS AF: 0.895 AC: 3108 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	6.7
Dann	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs985122; hg19: chr6-134931300; COSMIC: COSV69659140;