rs536331

chr6-137671912-T-C

Variant summary

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

The XR_943058.3(LOC105378018):n.525A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.445 in 151,926 control chromosomes in the GnomAD database, including 15,331 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 0.45 (15331 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: LOC105378018 XR_943058.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.11

Genes affected

LOC105378018 (HGNC:):

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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.527 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105378018	XR_943058.3	n.525A>G		non_coding_transcript_exon_variant	2/2
LINC03004	NR_125867.1	n.95-108T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC03004	ENST00000642830.1	n.426-108T>C		intron_variant, non_coding_transcript_variant
LINC03004	ENST00000691587.1	n.133-108T>C		intron_variant, non_coding_transcript_variant
LINC03004	ENST00000692965.2	n.266-108T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.445 AC: 67571 AN: 151808 Hom.: 15314 Cov.: 32

Gnomad AFR AF: 0.533

Gnomad AMI AF: 0.525

Gnomad AMR AF: 0.440

Gnomad ASJ AF: 0.485

Gnomad EAS AF: 0.303

Gnomad SAS AF: 0.356

Gnomad FIN AF: 0.344

Gnomad MID AF: 0.491

Gnomad NFE AF: 0.423

Gnomad OTH AF: 0.437

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

GnomAD4 genome AF: 0.445 AC: 67612 AN: 151926 Hom.: 15331 Cov.: 32 AF XY: 0.438 AC XY: 32547 AN XY: 74230

Gnomad4 AFR AF: 0.532

Gnomad4 AMR AF: 0.440

Gnomad4 ASJ AF: 0.485

Gnomad4 EAS AF: 0.302

Gnomad4 SAS AF: 0.356

Gnomad4 FIN AF: 0.344

Gnomad4 NFE AF: 0.423

Gnomad4 OTH AF: 0.433

Alfa AF: 0.436 Hom.: 8969

Bravo AF: 0.458

Asia WGS AF: 0.320 AC: 1110 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	7.1
Dann	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs536331; hg19: chr6-137993049; COSMIC: COSV71077366;