5-118073397-T-C

Position:

• chr5-118073397-T-C

Variant summary

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

The NR_104997.1(LINC02147):​n.170+148266T>C 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 0.4 in 151,718 control chromosomes in the GnomAD database, including 15,470 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 (15470 hom., cov: 30)
• Consequence: LINC02147 NR_104997.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.228

Genes affected

LINC02147 (HGNC:53007): (long intergenic non-protein coding RNA 2147)

LINC02208 (HGNC:52978): (long intergenic non-protein coding RNA 2208)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.956 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02147	NR_104997.1	n.170+148266T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02147	ENST00000509367.2	n.277-114068T>C		intron_variant, non_coding_transcript_variant		2
LINC02208	ENST00000660173.1	n.741-72333A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.400 AC: 60666 AN: 151602 Hom.: 15461 Cov.: 30

Gnomad AFR AF: 0.111

Gnomad AMI AF: 0.461

Gnomad AMR AF: 0.549

Gnomad ASJ AF: 0.472

Gnomad EAS AF: 0.978

Gnomad SAS AF: 0.587

Gnomad FIN AF: 0.558

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.457

Gnomad OTH AF: 0.409

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

GnomAD4 genome AF: 0.400 AC: 60676 AN: 151718 Hom.: 15470 Cov.: 30 AF XY: 0.413 AC XY: 30648 AN XY: 74128

Gnomad4 AFR AF: 0.111

Gnomad4 AMR AF: 0.550

Gnomad4 ASJ AF: 0.472

Gnomad4 EAS AF: 0.979

Gnomad4 SAS AF: 0.587

Gnomad4 FIN AF: 0.558

Gnomad4 NFE AF: 0.457

Gnomad4 OTH AF: 0.409

Alfa AF: 0.382 Hom.: 2377

Bravo AF: 0.387

Asia WGS AF: 0.717 AC: 2491 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.1
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2416504; hg19: chr5-117409092;