6-134523180-T-A

Position:

• chr6-134523180-T-A

Variant summary

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

The ENST00000650393.1(LINC03002):​n.2185+152A>T 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 0.718 in 152,126 control chromosomes in the GnomAD database, including 41,450 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 0.72 (41450 hom., cov: 32)
• Consequence: LINC03002 ENST00000650393.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.59

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=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.93 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	ENST00000650393.1	n.2185+152A>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.718 AC: 109088 AN: 152008 Hom.: 41427 Cov.: 32

Gnomad AFR AF: 0.444

Gnomad AMI AF: 0.771

Gnomad AMR AF: 0.832

Gnomad ASJ AF: 0.768

Gnomad EAS AF: 0.952

Gnomad SAS AF: 0.843

Gnomad FIN AF: 0.806

Gnomad MID AF: 0.690

Gnomad NFE AF: 0.814

Gnomad OTH AF: 0.721

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

GnomAD4 genome AF: 0.718 AC: 109154 AN: 152126 Hom.: 41450 Cov.: 32 AF XY: 0.723 AC XY: 53737 AN XY: 74374

Gnomad4 AFR AF: 0.444

Gnomad4 AMR AF: 0.832

Gnomad4 ASJ AF: 0.768

Gnomad4 EAS AF: 0.952

Gnomad4 SAS AF: 0.843

Gnomad4 FIN AF: 0.806

Gnomad4 NFE AF: 0.815

Gnomad4 OTH AF: 0.724

Alfa AF: 0.753 Hom.: 5521

Bravo AF: 0.709

Asia WGS AF: 0.871 AC: 3027 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	13
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1474827; hg19: chr6-134844318; COSMIC: COSV69766767;