chr6-134614626-G-T

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

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=-0.92).
• 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	ENST00000650393.1	n.136+57885C>A		intron_variant	Intron 2 of 8
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

Gnomad4 AFR AF: 0.499

Gnomad4 AMR AF: 0.693

Gnomad4 ASJ AF: 0.521

Gnomad4 EAS AF: 0.766

Gnomad4 SAS AF: 0.568

Gnomad4 FIN AF: 0.686

Gnomad4 NFE AF: 0.657

Gnomad4 OTH AF: 0.578

Alfa AF: 0.640 Hom.: 14243

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2223995; hg19: chr6-134935764;