chr6-44003090-G-A

Position:

• chr6-44003090-G-A

Variant summary

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

The NR_160955.1(LINC03040):​n.771G>A 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 0.0314 in 1,612,038 control chromosomes in the GnomAD database, including 2,058 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 0.041 (258 hom., cov: 33)
  • Exomes 𝑓: 0.030 (1800 hom.)
• Consequence: LINC03040 NR_160955.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.451

Genes affected

LINC03040 (HGNC:28692): (long intergenic non-protein coding RNA 3040)

SCIRT (HGNC:55341): (stem cell inhibitory RNA transcript)

POLR1C (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.58).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.219 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC03040	NR_160955.1	n.771G>A		non_coding_transcript_exon_variant	4/4
SCIRT	NR_125864.1	n.157-1974C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC03040	ENST00000336600.6	n.728G>A		non_coding_transcript_exon_variant	4/4	1
SCIRT	ENST00000687455.1	n.160-1974C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0410 AC: 6245 AN: 152160 Hom.: 258 Cov.: 33

Gnomad AFR AF: 0.0522

Gnomad AMI AF: 0.00658

Gnomad AMR AF: 0.0294

Gnomad ASJ AF: 0.0323

Gnomad EAS AF: 0.230

Gnomad SAS AF: 0.0988

Gnomad FIN AF: 0.0317

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0210

Gnomad OTH AF: 0.0368

GnomAD3 exomes AF: 0.0495 AC: 11891 AN: 240208 Hom.: 784 AF XY: 0.0510 AC XY: 6711 AN XY: 131636

Gnomad AFR exome AF: 0.0513

Gnomad AMR exome AF: 0.0149

Gnomad ASJ exome AF: 0.0337

Gnomad EAS exome AF: 0.241

Gnomad SAS exome AF: 0.0953

Gnomad FIN exome AF: 0.0288

Gnomad NFE exome AF: 0.0213

Gnomad OTH exome AF: 0.0385

GnomAD4 exome AF: 0.0303 AC: 44274 AN: 1459760 Hom.: 1800 Cov.: 34 AF XY: 0.0326 AC XY: 23681 AN XY: 726114

Gnomad4 AFR exome AF: 0.0580

Gnomad4 AMR exome AF: 0.0160

Gnomad4 ASJ exome AF: 0.0335

Gnomad4 EAS exome AF: 0.205

Gnomad4 SAS exome AF: 0.0966

Gnomad4 FIN exome AF: 0.0269

Gnomad4 NFE exome AF: 0.0182

Gnomad4 OTH exome AF: 0.0413

GnomAD4 genome AF: 0.0411 AC: 6265 AN: 152278 Hom.: 258 Cov.: 33 AF XY: 0.0433 AC XY: 3223 AN XY: 74444

Gnomad4 AFR AF: 0.0523

Gnomad4 AMR AF: 0.0294

Gnomad4 ASJ AF: 0.0323

Gnomad4 EAS AF: 0.230

Gnomad4 SAS AF: 0.0984

Gnomad4 FIN AF: 0.0317

Gnomad4 NFE AF: 0.0210

Gnomad4 OTH AF: 0.0402

Alfa AF: 0.0268 Hom.: 180

Bravo AF: 0.0404

Asia WGS AF: 0.139 AC: 483 AN: 3478

EpiCase AF: 0.0214

EpiControl AF: 0.0208

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.58
CADD	Benign	7.1
DANN	Uncertain	0.98

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.040		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs2295334; hg19: chr6-43970827; COSMIC: COSV60735403;