rs2295199

Positions:

• chr6-134454367-C-A

Variant summary

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

The NR_038216.1(LINC01010):​n.167-10374C>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 0.397 in 152,110 control chromosomes in the GnomAD database, including 13,020 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 0.40 (13019 hom., cov: 32)
  • Exomes 𝑓: 0.31 (1 hom.)
• Consequence: LINC01010 NR_038216.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.65

Genes affected

CT69 (HGNC:37196): (cancer/testis associated transcript 69)

LINC01010 (HGNC:48978): (long intergenic non-protein coding RNA 1010)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.482 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC01010	NR_038216.1	n.167-10374C>A		intron_variant, non_coding_transcript_variant
CT69	NR_125852.1	n.934+86G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CT69	ENST00000417483.5	n.316+86G>T		intron_variant, non_coding_transcript_variant		3
LINC01010	ENST00000431422.3	n.621-10374C>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.397 AC: 60305 AN: 151976 Hom.: 13013 Cov.: 32

Gnomad AFR AF: 0.229

Gnomad AMI AF: 0.362

Gnomad AMR AF: 0.369

Gnomad ASJ AF: 0.419

Gnomad EAS AF: 0.319

Gnomad SAS AF: 0.478

Gnomad FIN AF: 0.518

Gnomad MID AF: 0.434

Gnomad NFE AF: 0.486

Gnomad OTH AF: 0.385

GnomAD4 exome AF: 0.313 AC: 5 AN: 16 Hom.: 1 AF XY: 0.286 AC XY: 4 AN XY: 14

Gnomad4 ASJ exome AF: 0.00

Gnomad4 NFE exome AF: 0.333

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.397 AC: 60311 AN: 152094 Hom.: 13019 Cov.: 32 AF XY: 0.399 AC XY: 29684 AN XY: 74346

Gnomad4 AFR AF: 0.229

Gnomad4 AMR AF: 0.369

Gnomad4 ASJ AF: 0.419

Gnomad4 EAS AF: 0.319

Gnomad4 SAS AF: 0.479

Gnomad4 FIN AF: 0.518

Gnomad4 NFE AF: 0.486

Gnomad4 OTH AF: 0.384

Alfa AF: 0.467 Hom.: 34387

Bravo AF: 0.377

Asia WGS AF: 0.375 AC: 1305 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	0.10
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: rs2295199; hg19: chr6-134775505;