rs9321627

chr6-137701911-G-A

Variant summary

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

The ENST00000635999.1(LINC03004):n.433+27787G>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 0.189 in 152,160 control chromosomes in the GnomAD database, including 3,619 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 0.19 (3619 hom., cov: 32)
• Consequence: LINC03004 ENST00000635999.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0130

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=-0.76).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.513 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+27787G>A		intron_variant, non_coding_transcript_variant		5
LINC03004	ENST00000646621.1	n.601+13222G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.189 AC: 28763 AN: 152042 Hom.: 3621 Cov.: 32

Gnomad AFR AF: 0.0407

Gnomad AMI AF: 0.121

Gnomad AMR AF: 0.251

Gnomad ASJ AF: 0.186

Gnomad EAS AF: 0.528

Gnomad SAS AF: 0.284

Gnomad FIN AF: 0.305

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.216

Gnomad OTH AF: 0.207

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

GnomAD4 genome AF: 0.189 AC: 28747 AN: 152160 Hom.: 3619 Cov.: 32 AF XY: 0.198 AC XY: 14755 AN XY: 74394

Gnomad4 AFR AF: 0.0406

Gnomad4 AMR AF: 0.251

Gnomad4 ASJ AF: 0.186

Gnomad4 EAS AF: 0.529

Gnomad4 SAS AF: 0.283

Gnomad4 FIN AF: 0.305

Gnomad4 NFE AF: 0.216

Gnomad4 OTH AF: 0.205

Alfa AF: 0.218 Hom.: 769

Bravo AF: 0.177

Asia WGS AF: 0.380 AC: 1325 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
Cadd	Benign	0.83
Dann	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9321627; hg19: chr6-138023048; COSMIC: COSV68432211;