rs6935311

Variant names:

• chr6-134589900-A-G
• rs6935311
• ENST00000434593.1:n.89-58836T>C

Variant summary

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

The ENST00000434593.1(LINC03002):​n.89-58836T>C variant causes a intron 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 ENST00000434593.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.508
• Publications: 6 publications found

Genes affected

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

ENSG00000293692 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000434593.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC03002	ENST00000434593.1	TSL:3	n.89-58836T>C		intron	N/A
	LINC03002	ENST00000650393.2		n.137-49277T>C		intron	N/A
	LINC03002	ENST00000655921.2		n.106-49277T>C		intron	N/A

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

African (AFR) AF: 0.412 AC: 17080 AN: 41468

American (AMR) AF: 0.678 AC: 10365 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.518 AC: 1799 AN: 3470

East Asian (EAS) AF: 0.774 AC: 3999 AN: 5170

South Asian (SAS) AF: 0.570 AC: 2743 AN: 4814

European-Finnish (FIN) AF: 0.688 AC: 7270 AN: 10572

Middle Eastern (MID) AF: 0.412 AC: 121 AN: 294

European-Non Finnish (NFE) AF: 0.658 AC: 44715 AN: 68000

Other (OTH) AF: 0.553 AC: 1168 AN: 2112

Alfa AF: 0.630 Hom.: 23938

Bravo AF: 0.582

Asia WGS AF: 0.674 AC: 2343 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.98
DANN	Benign	0.57
PhyloP100		-0.51

Splicing

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

Other links and lift over

dbSNP: rs6935311; hg19: chr6-134911038;