6-137686393-G-T

Position:

• chr6-137686393-G-T

Variant summary

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

The ENST00000635999.1(LINC03004):​n.433+12269G>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 0.657 in 151,926 control chromosomes in the GnomAD database, including 33,243 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 0.66 (33243 hom., cov: 31)
• Consequence: LINC03004 ENST00000635999.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0930

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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.786 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC03004	ENST00000635999.1	n.433+12269G>T		intron_variant, non_coding_transcript_variant		5
LINC03004	ENST00000638039.1	n.439-701G>T		intron_variant, non_coding_transcript_variant		5
LINC03004	ENST00000646621.1	n.415-701G>T		intron_variant, non_coding_transcript_variant
LINC03004	ENST00000666119.1	n.393-701G>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.657 AC: 99691 AN: 151808 Hom.: 33207 Cov.: 31

Gnomad AFR AF: 0.762

Gnomad AMI AF: 0.482

Gnomad AMR AF: 0.624

Gnomad ASJ AF: 0.512

Gnomad EAS AF: 0.806

Gnomad SAS AF: 0.542

Gnomad FIN AF: 0.651

Gnomad MID AF: 0.547

Gnomad NFE AF: 0.608

Gnomad OTH AF: 0.655

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

GnomAD4 genome AF: 0.657 AC: 99774 AN: 151926 Hom.: 33243 Cov.: 31 AF XY: 0.657 AC XY: 48767 AN XY: 74260

Gnomad4 AFR AF: 0.762

Gnomad4 AMR AF: 0.624

Gnomad4 ASJ AF: 0.512

Gnomad4 EAS AF: 0.806

Gnomad4 SAS AF: 0.541

Gnomad4 FIN AF: 0.651

Gnomad4 NFE AF: 0.608

Gnomad4 OTH AF: 0.655

Alfa AF: 0.612 Hom.: 38012

Bravo AF: 0.657

Asia WGS AF: 0.687 AC: 2389 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	0.35
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs636393; hg19: chr6-138007530;