6-137658834-C-T

Variant names:

• chr6-137658834-C-T
• rs686851
• ENST00000642830.1:n.38+799C>T

Variant summary

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

The ENST00000642830.1(LINC03004):​n.38+799C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.537 in 151,986 control chromosomes in the GnomAD database, including 21,954 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 0.54 (21954 hom., cov: 32)
• Consequence: LINC03004 ENST00000642830.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.657

Genes affected

LINC03004 (HGNC:56128): (long intergenic non-protein coding RNA 3004)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.578 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
LINC03004	ENST00000642830.1	n.38+799C>T		intron_variant	Intron 1 of 6
LINC03004	ENST00000691587.1	n.38+799C>T		intron_variant	Intron 1 of 4
LINC03004	ENST00000692965.2	n.38+799C>T		intron_variant	Intron 1 of 5

Frequencies

GnomAD3 genomes AF: 0.537 AC: 81604 AN: 151868 Hom.: 21921 Cov.: 32

Gnomad AFR AF: 0.584

Gnomad AMI AF: 0.643

Gnomad AMR AF: 0.562

Gnomad ASJ AF: 0.591

Gnomad EAS AF: 0.472

Gnomad SAS AF: 0.510

Gnomad FIN AF: 0.447

Gnomad MID AF: 0.608

Gnomad NFE AF: 0.520

Gnomad OTH AF: 0.520

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

GnomAD4 genome AF: 0.537 AC: 81688 AN: 151986 Hom.: 21954 Cov.: 32 AF XY: 0.533 AC XY: 39601 AN XY: 74286

Gnomad4 AFR AF: 0.584

Gnomad4 AMR AF: 0.563

Gnomad4 ASJ AF: 0.591

Gnomad4 EAS AF: 0.471

Gnomad4 SAS AF: 0.512

Gnomad4 FIN AF: 0.447

Gnomad4 NFE AF: 0.520

Gnomad4 OTH AF: 0.522

Alfa AF: 0.524 Hom.: 11485

Bravo AF: 0.548

Asia WGS AF: 0.480 AC: 1666 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.0
DANN	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs686851; hg19: chr6-137979971;