rs1479211

chr5-118230595-A-G

Variant summary

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

The NR_104997.1(LINC02147):n.171-34759A>G 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 0.416 in 151,972 control chromosomes in the GnomAD database, including 15,469 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 0.42 (15469 hom., cov: 31)
• Consequence: LINC02147 NR_104997.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.546

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=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.652 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02147	NR_104997.1	n.171-34759A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02147	ENST00000509367.2	n.404-34759A>G		intron_variant, non_coding_transcript_variant		2
LINC02208	ENST00000660173.1	n.688-79134T>C		intron_variant, non_coding_transcript_variant
LINC02147	ENST00000661774.1	n.277-34759A>G		intron_variant, non_coding_transcript_variant
LINC02208	ENST00000666092.1	n.393-79134T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.416 AC: 63143 AN: 151854 Hom.: 15446 Cov.: 31

Gnomad AFR AF: 0.658

Gnomad AMI AF: 0.487

Gnomad AMR AF: 0.351

Gnomad ASJ AF: 0.447

Gnomad EAS AF: 0.0224

Gnomad SAS AF: 0.237

Gnomad FIN AF: 0.194

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.356

Gnomad OTH AF: 0.443

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

GnomAD4 genome AF: 0.416 AC: 63212 AN: 151972 Hom.: 15469 Cov.: 31 AF XY: 0.402 AC XY: 29895 AN XY: 74292

Gnomad4 AFR AF: 0.658

Gnomad4 AMR AF: 0.350

Gnomad4 ASJ AF: 0.447

Gnomad4 EAS AF: 0.0223

Gnomad4 SAS AF: 0.236

Gnomad4 FIN AF: 0.194

Gnomad4 NFE AF: 0.356

Gnomad4 OTH AF: 0.443

Alfa AF: 0.376 Hom.: 21016

Bravo AF: 0.442

Asia WGS AF: 0.203 AC: 708 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	0.37
Dann	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1479211; hg19: chr5-117566290;