rs9366778

chr6-31301396-G-A

Variant summary

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

The NR_149115.1(LINC02571):n.166+76C>T 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 0.473 in 150,880 control chromosomes in the GnomAD database, including 17,537 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 0.47 (17536 hom., cov: 31)
  • Exomes 𝑓: 0.40 (1 hom.)
• Consequence: LINC02571 NR_149115.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.913

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=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.6 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02571	NR_149115.1	n.166+76C>T		intron_variant, non_coding_transcript_variant
LOC112267902	XR_926691.3	n.1060+363C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02571	ENST00000539514.1	n.171+76C>T		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.473 AC: 71321 AN: 150752 Hom.: 17513 Cov.: 31

Gnomad AFR AF: 0.533

Gnomad AMI AF: 0.320

Gnomad AMR AF: 0.549

Gnomad ASJ AF: 0.396

Gnomad EAS AF: 0.617

Gnomad SAS AF: 0.609

Gnomad FIN AF: 0.516

Gnomad MID AF: 0.564

Gnomad NFE AF: 0.398

Gnomad OTH AF: 0.493

GnomAD4 exome AF: 0.400 AC: 4 AN: 10 Hom.: 1 AF XY: 0.400 AC XY: 4 AN XY: 10

Gnomad4 NFE exome AF: 0.375

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.473 AC: 71395 AN: 150870 Hom.: 17536 Cov.: 31 AF XY: 0.483 AC XY: 35596 AN XY: 73700

Gnomad4 AFR AF: 0.532

Gnomad4 AMR AF: 0.550

Gnomad4 ASJ AF: 0.396

Gnomad4 EAS AF: 0.618

Gnomad4 SAS AF: 0.609

Gnomad4 FIN AF: 0.516

Gnomad4 NFE AF: 0.398

Gnomad4 OTH AF: 0.494

Alfa AF: 0.423 Hom.: 17144

Bravo AF: 0.477

Asia WGS AF: 0.618 AC: 2149 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	7.1
Dann	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9366778; hg19: chr6-31269173;