10-42980330-T-G

Position:

• chr10-42980330-T-G

Variant summary

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

The NR_126352.1(LINC01264):​n.370A>C 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 0.256 in 152,216 control chromosomes in the GnomAD database, including 5,194 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 0.26 (5191 hom., cov: 33)
  • Exomes 𝑓: 0.39 (3 hom.)
• Consequence: LINC01264 NR_126352.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.115

Genes affected

LINC01264 (HGNC:50282): (long intergenic non-protein coding RNA 1264)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.282 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01264	NR_126352.1	n.370A>C		non_coding_transcript_exon_variant	2/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01264	ENST00000431395.1	n.370A>C		non_coding_transcript_exon_variant	2/3	3

Frequencies

GnomAD3 genomes AF: 0.256 AC: 38862 AN: 152052 Hom.: 5179 Cov.: 33

Gnomad AFR AF: 0.286

Gnomad AMI AF: 0.224

Gnomad AMR AF: 0.216

Gnomad ASJ AF: 0.336

Gnomad EAS AF: 0.00174

Gnomad SAS AF: 0.153

Gnomad FIN AF: 0.280

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.265

Gnomad OTH AF: 0.253

GnomAD4 exome AF: 0.391 AC: 18 AN: 46 Hom.: 3 Cov.: 0 AF XY: 0.412 AC XY: 14 AN XY: 34

Gnomad4 AFR exome AF: 0.00

Gnomad4 FIN exome AF: 0.500

Gnomad4 NFE exome AF: 0.447

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.256 AC: 38906 AN: 152170 Hom.: 5191 Cov.: 33 AF XY: 0.252 AC XY: 18746 AN XY: 74394

Gnomad4 AFR AF: 0.286

Gnomad4 AMR AF: 0.216

Gnomad4 ASJ AF: 0.336

Gnomad4 EAS AF: 0.00174

Gnomad4 SAS AF: 0.152

Gnomad4 FIN AF: 0.280

Gnomad4 NFE AF: 0.265

Gnomad4 OTH AF: 0.250

Alfa AF: 0.165 Hom.: 342

Bravo AF: 0.253

Asia WGS AF: 0.100 AC: 353 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.4
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11239851; hg19: chr10-43475778;