6-137701403-T-G

Position:

• chr6-137701403-T-G

Variant summary

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

The ENST00000635999.1(LINC03004):​n.433+27279T>G 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 0.482 in 152,056 control chromosomes in the GnomAD database, including 18,558 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 0.48 (18558 hom., cov: 32)
• Consequence: LINC03004 ENST00000635999.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.30

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=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.777 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+27279T>G		intron_variant, non_coding_transcript_variant		5
LINC03004	ENST00000646621.1	n.601+12714T>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.483 AC: 73332 AN: 151938 Hom.: 18550 Cov.: 32

Gnomad AFR AF: 0.613

Gnomad AMI AF: 0.320

Gnomad AMR AF: 0.444

Gnomad ASJ AF: 0.380

Gnomad EAS AF: 0.798

Gnomad SAS AF: 0.436

Gnomad FIN AF: 0.472

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.400

Gnomad OTH AF: 0.489

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

GnomAD4 genome AF: 0.482 AC: 73366 AN: 152056 Hom.: 18558 Cov.: 32 AF XY: 0.486 AC XY: 36133 AN XY: 74330

Gnomad4 AFR AF: 0.613

Gnomad4 AMR AF: 0.443

Gnomad4 ASJ AF: 0.380

Gnomad4 EAS AF: 0.798

Gnomad4 SAS AF: 0.434

Gnomad4 FIN AF: 0.472

Gnomad4 NFE AF: 0.400

Gnomad4 OTH AF: 0.483

Alfa AF: 0.413 Hom.: 26647

Bravo AF: 0.486

Asia WGS AF: 0.593 AC: 2061 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	0.76
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs647108; hg19: chr6-138022540; COSMIC: COSV68432206;