rs12900200

Positions:

• chr15-101613601-A-G

Variant summary

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

The ENST00000618724.2(LINC02348):​n.608T>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 0.463 in 152,094 control chromosomes in the GnomAD database, including 16,812 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 0.46 (16798 hom., cov: 32)
  • Exomes 𝑓: 0.47 (14 hom.)
• Consequence: LINC02348 ENST00000618724.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00300

Genes affected

LINC02348 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.51 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC02348	NR_147041.1	n.564T>C		non_coding_transcript_exon_variant	2/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02348	ENST00000618724.2	n.608T>C		non_coding_transcript_exon_variant	2/3	4
LINC02348	ENST00000655738.1	n.756T>C		non_coding_transcript_exon_variant	2/3

Frequencies

GnomAD3 genomes AF: 0.463 AC: 70305 AN: 151838 Hom.: 16773 Cov.: 32

Gnomad AFR AF: 0.516

Gnomad AMI AF: 0.509

Gnomad AMR AF: 0.336

Gnomad ASJ AF: 0.308

Gnomad EAS AF: 0.241

Gnomad SAS AF: 0.415

Gnomad FIN AF: 0.476

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.487

Gnomad OTH AF: 0.411

GnomAD4 exome AF: 0.471 AC: 65 AN: 138 Hom.: 14 AF XY: 0.480 AC XY: 49 AN XY: 102

Gnomad4 AFR exome AF: 0.750

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.500

Gnomad4 NFE exome AF: 0.509

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.463 AC: 70373 AN: 151956 Hom.: 16798 Cov.: 32 AF XY: 0.460 AC XY: 34135 AN XY: 74258

Gnomad4 AFR AF: 0.516

Gnomad4 AMR AF: 0.335

Gnomad4 ASJ AF: 0.308

Gnomad4 EAS AF: 0.241

Gnomad4 SAS AF: 0.414

Gnomad4 FIN AF: 0.476

Gnomad4 NFE AF: 0.487

Gnomad4 OTH AF: 0.415

Alfa AF: 0.459 Hom.: 3490

Bravo AF: 0.448

Asia WGS AF: 0.373 AC: 1297 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.4
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12900200; hg19: chr15-102153804; COSMIC: COSV61751269;