chr15-97396008-T-C

Variant names:

• chr15-97396008-T-C
• rs4555132
• ENST00000558621.2:n.755+1649A>G

Variant summary

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

The ENST00000658446.1(LINC02254):​n.639A>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 0.231 in 152,092 control chromosomes in the GnomAD database, including 4,165 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 0.23 (4165 hom., cov: 32)
• Consequence: LINC02254 ENST00000658446.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.18

Genes affected

LINC02254 (HGNC:):

LINC02253 (HGNC:53151): (long intergenic non-protein coding RNA 2253)

LINC02254 (HGNC:53152): (long intergenic non-protein coding RNA 2254)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.25 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02254	NR_120324.1	n.755+1649A>G		intron_variant	Intron 4 of 4
LINC02253	NR_183853.1	n.293-15184T>C		intron_variant	Intron 2 of 5
LINC02253	NR_183854.1	n.293-15184T>C		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02254	ENST00000558621.2	n.755+1649A>G		intron_variant	Intron 4 of 4	1
LINC02254	ENST00000658446.1	n.639A>G		non_coding_transcript_exon_variant	Exon 5 of 5
LINC02253	ENST00000559321.2	n.251-15184T>C		intron_variant	Intron 3 of 5	2

Frequencies

GnomAD3 genomes AF: 0.232 AC: 35193 AN: 151974 Hom.: 4160 Cov.: 32

Gnomad AFR AF: 0.205

Gnomad AMI AF: 0.184

Gnomad AMR AF: 0.247

Gnomad ASJ AF: 0.209

Gnomad EAS AF: 0.106

Gnomad SAS AF: 0.172

Gnomad FIN AF: 0.271

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.253

Gnomad OTH AF: 0.243

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.231 AC: 35203 AN: 152092 Hom.: 4165 Cov.: 32 AF XY: 0.230 AC XY: 17135 AN XY: 74346

Gnomad4 AFR AF: 0.204 AC: 0.204356 AN: 0.204356

Gnomad4 AMR AF: 0.248 AC: 0.247839 AN: 0.247839

Gnomad4 ASJ AF: 0.209 AC: 0.208646 AN: 0.208646

Gnomad4 EAS AF: 0.106 AC: 0.106243 AN: 0.106243

Gnomad4 SAS AF: 0.171 AC: 0.170889 AN: 0.170889

Gnomad4 FIN AF: 0.271 AC: 0.271242 AN: 0.271242

Gnomad4 NFE AF: 0.253 AC: 0.253494 AN: 0.253494

Gnomad4 OTH AF: 0.240 AC: 0.240284 AN: 0.240284

Alfa AF: 0.248 Hom.: 7990

Bravo AF: 0.229

Asia WGS AF: 0.125 AC: 435 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.14
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4555132; hg19: chr15-97939238;