rs10079352

Positions:

• chr5-118158945-G-A

Variant summary

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

The NR_104997.1(LINC02147):​n.171-106409G>A 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 0.596 in 151,880 control chromosomes in the GnomAD database, including 30,369 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 0.60 (30369 hom., cov: 31)
• Consequence: LINC02147 NR_104997.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.276

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=-0.66).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.881 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02147	NR_104997.1	n.171-106409G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02147	ENST00000509367.2	n.277-28520G>A		intron_variant, non_coding_transcript_variant		2
LINC02208	ENST00000660173.1	n.688-7484C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.595 AC: 90343 AN: 151762 Hom.: 30313 Cov.: 31

Gnomad AFR AF: 0.889

Gnomad AMI AF: 0.603

Gnomad AMR AF: 0.451

Gnomad ASJ AF: 0.541

Gnomad EAS AF: 0.0218

Gnomad SAS AF: 0.401

Gnomad FIN AF: 0.416

Gnomad MID AF: 0.699

Gnomad NFE AF: 0.536

Gnomad OTH AF: 0.597

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

GnomAD4 genome AF: 0.596 AC: 90449 AN: 151880 Hom.: 30369 Cov.: 31 AF XY: 0.582 AC XY: 43143 AN XY: 74188

Gnomad4 AFR AF: 0.889

Gnomad4 AMR AF: 0.450

Gnomad4 ASJ AF: 0.541

Gnomad4 EAS AF: 0.0216

Gnomad4 SAS AF: 0.400

Gnomad4 FIN AF: 0.416

Gnomad4 NFE AF: 0.536

Gnomad4 OTH AF: 0.596

Alfa AF: 0.536 Hom.: 49860

Bravo AF: 0.611

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	8.2
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10079352; hg19: chr5-117494640;