rs3873385

chr6-31301531-C-T

Variant summary

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

The NR_149115.1(LINC02571):n.107G>A 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 0.141 in 151,988 control chromosomes in the GnomAD database, including 1,764 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 0.14 (1764 hom., cov: 32)
  • Exomes 𝑓: 0.083 (0 hom.)
• Consequence: LINC02571 NR_149115.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.194

Genes affected

LINC02571 (HGNC:53630): (long intergenic non-protein coding RNA 2571)

LOC112267902 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.3 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02571	NR_149115.1	n.107G>A		non_coding_transcript_exon_variant	1/4
LOC112267902	XR_926691.3	n.1060+228G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02571	ENST00000539514.1	n.112G>A		non_coding_transcript_exon_variant	1/4	4

Frequencies

GnomAD3 genomes AF: 0.141 AC: 21439 AN: 151858 Hom.: 1761 Cov.: 32

Gnomad AFR AF: 0.110

Gnomad AMI AF: 0.135

Gnomad AMR AF: 0.171

Gnomad ASJ AF: 0.179

Gnomad EAS AF: 0.313

Gnomad SAS AF: 0.113

Gnomad FIN AF: 0.0739

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.151

Gnomad OTH AF: 0.167

GnomAD4 exome AF: 0.0833 AC: 1 AN: 12 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 8

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.500

Gnomad4 NFE exome AF: 0.00

GnomAD4 genome AF: 0.141 AC: 21450 AN: 151976 Hom.: 1764 Cov.: 32 AF XY: 0.137 AC XY: 10205 AN XY: 74296

Gnomad4 AFR AF: 0.109

Gnomad4 AMR AF: 0.170

Gnomad4 ASJ AF: 0.179

Gnomad4 EAS AF: 0.313

Gnomad4 SAS AF: 0.113

Gnomad4 FIN AF: 0.0739

Gnomad4 NFE AF: 0.151

Gnomad4 OTH AF: 0.171

Alfa AF: 0.150 Hom.: 1978

Bravo AF: 0.150

Asia WGS AF: 0.183 AC: 637 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	5.8
Dann	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3873385; hg19: chr6-31269308;