rs11255149

Positions:

• chr10-7469641-T-C

Variant summary

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

The NR_184109.1(LINC02642):​n.81-48A>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 0.0528 in 152,274 control chromosomes in the GnomAD database, including 308 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 0.053 (308 hom., cov: 32)
  • Exomes 𝑓: 0.17 (0 hom.)
• Consequence: LINC02642 NR_184109.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0710

Genes affected

LINC02642 (HGNC:54124): (long intergenic non-protein coding RNA 2642)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.079 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02642	NR_184109.1	n.81-48A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02642	ENST00000670632.2	n.186+45A>G		intron_variant, non_coding_transcript_variant
LINC02642	ENST00000420395.1	n.33-48A>G		intron_variant, non_coding_transcript_variant		3
LINC02642	ENST00000660269.1	n.111-48A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0528 AC: 8040 AN: 152150 Hom.: 307 Cov.: 32

Gnomad AFR AF: 0.0145

Gnomad AMI AF: 0.161

Gnomad AMR AF: 0.0582

Gnomad ASJ AF: 0.0865

Gnomad EAS AF: 0.00192

Gnomad SAS AF: 0.0851

Gnomad FIN AF: 0.0294

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.0762

Gnomad OTH AF: 0.0722

GnomAD4 exome AF: 0.167 AC: 1 AN: 6 Hom.: 0 Cov.: 0 AF XY: 0.167 AC XY: 1 AN XY: 6

Gnomad4 AFR exome AF: 0.00

Gnomad4 NFE exome AF: 0.250

GnomAD4 genome AF: 0.0528 AC: 8038 AN: 152268 Hom.: 308 Cov.: 32 AF XY: 0.0521 AC XY: 3883 AN XY: 74472

Gnomad4 AFR AF: 0.0144

Gnomad4 AMR AF: 0.0581

Gnomad4 ASJ AF: 0.0865

Gnomad4 EAS AF: 0.00193

Gnomad4 SAS AF: 0.0858

Gnomad4 FIN AF: 0.0294

Gnomad4 NFE AF: 0.0762

Gnomad4 OTH AF: 0.0715

Alfa AF: 0.0753 Hom.: 628

Bravo AF: 0.0528

Asia WGS AF: 0.0300 AC: 104 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	4.5
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11255149; hg19: chr10-7511603;