6-134610162-A-G

Variant names:

• chr6-134610162-A-G
• rs985122
• ENST00000434593.1:n.88+49587T>C

Variant summary

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

The ENST00000434593.1(LINC03002):​n.88+49587T>C variant causes a intron 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 ENST00000434593.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.71
• Publications: 3 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=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.975 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

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC03002	ENST00000434593.1	TSL:3	n.88+49587T>C		intron	N/A
	LINC03002	ENST00000650393.2		n.136+62349T>C		intron	N/A
	LINC03002	ENST00000655921.2		n.106-69539T>C		intron	N/A

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

African (AFR) AF: 0.867 AC: 35976 AN: 41484

American (AMR) AF: 0.846 AC: 12944 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.737 AC: 2554 AN: 3464

East Asian (EAS) AF: 0.998 AC: 5170 AN: 5182

South Asian (SAS) AF: 0.769 AC: 3705 AN: 4816

European-Finnish (FIN) AF: 0.812 AC: 8578 AN: 10570

Middle Eastern (MID) AF: 0.680 AC: 200 AN: 294

European-Non Finnish (NFE) AF: 0.793 AC: 53928 AN: 67998

Other (OTH) AF: 0.791 AC: 1670 AN: 2110

Alfa AF: 0.792 Hom.: 21606

Bravo AF: 0.828

Asia WGS AF: 0.895 AC: 3108 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	6.7
DANN	Benign	0.70
PhyloP100		1.7

Splicing

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

Other links and lift over

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