chr6-134577318-C-T

Variant names:

• chr6-134577318-C-T
• rs228437
• ENST00000434593.1:n.89-46254G>A

Variant summary

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

The ENST00000434593.1(LINC03002):​n.89-46254G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.815 in 152,000 control chromosomes in the GnomAD database, including 50,722 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 0.81 (50722 hom., cov: 32)
• Consequence: LINC03002 ENST00000434593.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.472
• Publications: 13 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=-0.88).
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC03002	ENST00000434593.1	n.89-46254G>A		intron_variant	Intron 1 of 2	3
LINC03002	ENST00000650393.2	n.137-36695G>A		intron_variant	Intron 2 of 5
LINC03002	ENST00000655921.2	n.106-36695G>A		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.815 AC: 123736 AN: 151882 Hom.: 50669 Cov.: 32

Gnomad AFR AF: 0.840

Gnomad AMI AF: 0.555

Gnomad AMR AF: 0.843

Gnomad ASJ AF: 0.738

Gnomad EAS AF: 0.997

Gnomad SAS AF: 0.768

Gnomad FIN AF: 0.811

Gnomad MID AF: 0.677

Gnomad NFE AF: 0.792

Gnomad OTH AF: 0.781

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

GnomAD4 genome AF: 0.815 AC: 123848 AN: 152000 Hom.: 50722 Cov.: 32 AF XY: 0.816 AC XY: 60576 AN XY: 74276

African (AFR) AF: 0.840 AC: 34850 AN: 41484

American (AMR) AF: 0.843 AC: 12865 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.738 AC: 2555 AN: 3464

East Asian (EAS) AF: 0.997 AC: 5171 AN: 5184

South Asian (SAS) AF: 0.768 AC: 3698 AN: 4818

European-Finnish (FIN) AF: 0.811 AC: 8573 AN: 10572

Middle Eastern (MID) AF: 0.677 AC: 199 AN: 294

European-Non Finnish (NFE) AF: 0.792 AC: 53776 AN: 67900

Other (OTH) AF: 0.784 AC: 1656 AN: 2112

Alfa AF: 0.756 Hom.: 24518

Bravo AF: 0.819

Asia WGS AF: 0.897 AC: 3117 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.8
DANN	Benign	0.35
PhyloP100		0.47

Splicing

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

Other links and lift over

dbSNP: rs228437; hg19: chr6-134898456;