rs6921233

chr6-137679978-G-Achr6-137679978-G-C

Variant summary

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

The ENST00000635999.1(LINC03004):n.433+5854G>A 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 0.491 in 152,008 control chromosomes in the GnomAD database, including 18,384 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 0.49 (18384 hom., cov: 32)
• Consequence: LINC03004 ENST00000635999.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.602

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=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.529 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC03004	ENST00000635999.1	n.433+5854G>A		intron_variant, non_coding_transcript_variant		5
LINC03004	ENST00000638039.1	n.438+5854G>A		intron_variant, non_coding_transcript_variant		5
LINC03004	ENST00000646621.1	n.414+5854G>A		intron_variant, non_coding_transcript_variant
LINC03004	ENST00000666119.1	n.392+5854G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.491 AC: 74588 AN: 151890 Hom.: 18382 Cov.: 32

Gnomad AFR AF: 0.535

Gnomad AMI AF: 0.357

Gnomad AMR AF: 0.453

Gnomad ASJ AF: 0.392

Gnomad EAS AF: 0.535

Gnomad SAS AF: 0.449

Gnomad FIN AF: 0.547

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.471

Gnomad OTH AF: 0.503

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

GnomAD4 genome AF: 0.491 AC: 74609 AN: 152008 Hom.: 18384 Cov.: 32 AF XY: 0.494 AC XY: 36676 AN XY: 74278

Gnomad4 AFR AF: 0.535

Gnomad4 AMR AF: 0.452

Gnomad4 ASJ AF: 0.392

Gnomad4 EAS AF: 0.536

Gnomad4 SAS AF: 0.447

Gnomad4 FIN AF: 0.547

Gnomad4 NFE AF: 0.471

Gnomad4 OTH AF: 0.498

Alfa AF: 0.470 Hom.: 16374

Bravo AF: 0.485

Asia WGS AF: 0.484 AC: 1686 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	6.7
Dann	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6921233; hg19: chr6-138001115;