chr15-101613601-A-G

Variant names:

• chr15-101613601-A-G
• rs12900200
• ENST00000618724.3:n.608T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000618724.3(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 ENST00000618724.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00300
• Publications: 3 publications found

Genes affected

LINC02348 (HGNC:53270): (long intergenic non-protein coding RNA 2348)

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000618724.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02348	NR_147041.1		n.564T>C		non_coding_transcript_exon	Exon 2 of 3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02348	ENST00000618724.3	TSL:4	n.608T>C		non_coding_transcript_exon	Exon 2 of 3
	LINC02348	ENST00000655738.1		n.756T>C		non_coding_transcript_exon	Exon 2 of 3
	LINC02348	ENST00000740832.1		n.189+2407T>C		intron	N/A

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

African (AFR) AF: 0.750 AC: 3 AN: 4

American (AMR) AF: 0.00 AC: 0 AN: 2

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2

East Asian (EAS) AF: 0.00 AC: 0 AN: 4

South Asian (SAS) AF: 0.00 AC: 0 AN: 4

European-Finnish (FIN) AF: 0.500 AC: 1 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.509 AC: 59 AN: 116

Other (OTH) AF: 0.500 AC: 2 AN: 4

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

African (AFR) AF: 0.516 AC: 21391 AN: 41442

American (AMR) AF: 0.335 AC: 5121 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.308 AC: 1069 AN: 3468

East Asian (EAS) AF: 0.241 AC: 1243 AN: 5162

South Asian (SAS) AF: 0.414 AC: 1995 AN: 4816

European-Finnish (FIN) AF: 0.476 AC: 5024 AN: 10546

Middle Eastern (MID) AF: 0.269 AC: 79 AN: 294

European-Non Finnish (NFE) AF: 0.487 AC: 33114 AN: 67928

Other (OTH) AF: 0.415 AC: 875 AN: 2110

Alfa AF: 0.451 Hom.: 5985

Bravo AF: 0.448

Asia WGS AF: 0.373 AC: 1297 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.4
DANN	Benign	0.46
PhyloP100		-0.0030

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs12900200;

hg19: chr15-102153804;

COSMIC: COSV61751269;