6-134614626-G-T

Variant names:

• chr6-134614626-G-T
• rs2223995
• ENST00000434593.1:n.88+45123C>A

Variant summary

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

The ENST00000434593.1(LINC03002):​n.88+45123C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.615 in 151,978 control chromosomes in the GnomAD database, including 29,402 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 0.61 (29402 hom., cov: 32)
• Consequence: LINC03002 ENST00000434593.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.99
• 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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.746 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.88+45123C>A		intron_variant	Intron 1 of 2	3
LINC03002	ENST00000650393.2	n.136+57885C>A		intron_variant	Intron 2 of 5
LINC03002	ENST00000655921.2	n.106-74003C>A		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.615 AC: 93407 AN: 151860 Hom.: 29389 Cov.: 32

Gnomad AFR AF: 0.499

Gnomad AMI AF: 0.490

Gnomad AMR AF: 0.693

Gnomad ASJ AF: 0.521

Gnomad EAS AF: 0.766

Gnomad SAS AF: 0.570

Gnomad FIN AF: 0.686

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.657

Gnomad OTH AF: 0.575

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

GnomAD4 genome AF: 0.615 AC: 93463 AN: 151978 Hom.: 29402 Cov.: 32 AF XY: 0.618 AC XY: 45937 AN XY: 74280

African (AFR) AF: 0.499 AC: 20678 AN: 41416

American (AMR) AF: 0.693 AC: 10590 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.521 AC: 1805 AN: 3466

East Asian (EAS) AF: 0.766 AC: 3947 AN: 5154

South Asian (SAS) AF: 0.568 AC: 2740 AN: 4820

European-Finnish (FIN) AF: 0.686 AC: 7244 AN: 10554

Middle Eastern (MID) AF: 0.425 AC: 125 AN: 294

European-Non Finnish (NFE) AF: 0.657 AC: 44665 AN: 67970

Other (OTH) AF: 0.578 AC: 1222 AN: 2116

Alfa AF: 0.638 Hom.: 15946

Bravo AF: 0.612

Asia WGS AF: 0.678 AC: 2355 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.061
DANN	Benign	0.70
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs2223995; hg19: chr6-134935764;