rs6935311

Positions:

• chr6-134589900-A-G

Variant summary

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

The ENST00000655921.2(LINC03002):​n.106-49277T>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 0.59 in 152,100 control chromosomes in the GnomAD database, including 27,684 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 0.59 (27684 hom., cov: 32)
• Consequence: LINC03002 ENST00000655921.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.508

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=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.753 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC03002	ENST00000655921.2	n.106-49277T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.590 AC: 89650 AN: 151982 Hom.: 27664 Cov.: 32

Gnomad AFR AF: 0.412

Gnomad AMI AF: 0.496

Gnomad AMR AF: 0.678

Gnomad ASJ AF: 0.518

Gnomad EAS AF: 0.774

Gnomad SAS AF: 0.571

Gnomad FIN AF: 0.688

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.658

Gnomad OTH AF: 0.550

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

GnomAD4 genome AF: 0.590 AC: 89712 AN: 152100 Hom.: 27684 Cov.: 32 AF XY: 0.594 AC XY: 44196 AN XY: 74344

Gnomad4 AFR AF: 0.412

Gnomad4 AMR AF: 0.678

Gnomad4 ASJ AF: 0.518

Gnomad4 EAS AF: 0.774

Gnomad4 SAS AF: 0.570

Gnomad4 FIN AF: 0.688

Gnomad4 NFE AF: 0.658

Gnomad4 OTH AF: 0.553

Alfa AF: 0.630 Hom.: 17139

Bravo AF: 0.582

Asia WGS AF: 0.674 AC: 2343 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.98
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6935311; hg19: chr6-134911038;