chr12-62603400-T-C

Position:

• chr12-62603400-T-C

Variant summary

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

The NR_121682.1(LINC01465):​n.35A>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 0.412 in 1,189,168 control chromosomes in the GnomAD database, including 101,417 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 0.42 (13471 hom., cov: 32)
  • Exomes 𝑓: 0.41 (87946 hom.)
• Consequence: LINC01465 NR_121682.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.574

Genes affected

LINC01465 (HGNC:26364): (long intergenic non-protein coding RNA 1465)

(HGNC:):

MIRLET7IHG (HGNC:55478): (MIRLET7I host gene)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.475 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC01465	NR_121682.1	n.35A>G		non_coding_transcript_exon_variant	1/1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01465	ENST00000408887.3	n.291A>G		non_coding_transcript_exon_variant	1/1
	ENST00000619323.2	n.35T>C		non_coding_transcript_exon_variant	1/1
MIRLET7IHG	ENST00000550290.2	n.84+565T>C		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.418 AC: 63409 AN: 151790 Hom.: 13463 Cov.: 32

Gnomad AFR AF: 0.481

Gnomad AMI AF: 0.357

Gnomad AMR AF: 0.370

Gnomad ASJ AF: 0.502

Gnomad EAS AF: 0.347

Gnomad SAS AF: 0.389

Gnomad FIN AF: 0.377

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.400

Gnomad OTH AF: 0.423

GnomAD4 exome AF: 0.411 AC: 426123 AN: 1037262 Hom.: 87946 Cov.: 23 AF XY: 0.411 AC XY: 205462 AN XY: 500336

Gnomad4 AFR exome AF: 0.477

Gnomad4 AMR exome AF: 0.343

Gnomad4 ASJ exome AF: 0.501

Gnomad4 EAS exome AF: 0.356

Gnomad4 SAS exome AF: 0.392

Gnomad4 FIN exome AF: 0.362

Gnomad4 NFE exome AF: 0.412

Gnomad4 OTH exome AF: 0.417

GnomAD4 genome AF: 0.418 AC: 63441 AN: 151906 Hom.: 13471 Cov.: 32 AF XY: 0.413 AC XY: 30684 AN XY: 74274

Gnomad4 AFR AF: 0.481

Gnomad4 AMR AF: 0.370

Gnomad4 ASJ AF: 0.502

Gnomad4 EAS AF: 0.347

Gnomad4 SAS AF: 0.389

Gnomad4 FIN AF: 0.377

Gnomad4 NFE AF: 0.400

Gnomad4 OTH AF: 0.418

Alfa AF: 0.402 Hom.: 1566

Bravo AF: 0.421

Asia WGS AF: 0.330 AC: 1143 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.8
DANN	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10877887; hg19: chr12-62997180;