rs3915971

Positions:

• chr6-31301571-A-G

Variant summary

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

The NR_149115.1(LINC02571):​n.67T>C 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 0.238 in 152,092 control chromosomes in the GnomAD database, including 4,434 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 0.24 (4432 hom., cov: 32)
  • Exomes 𝑓: 0.24 (2 hom.)
• Consequence: LINC02571 NR_149115.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.219

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=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.307 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02571	NR_149115.1	n.67T>C		non_coding_transcript_exon_variant	1/4
LOC112267902	XR_926691.3	n.1060+188T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02571	ENST00000539514.1	n.72T>C		non_coding_transcript_exon_variant	1/4	4

Frequencies

GnomAD3 genomes AF: 0.238 AC: 36133 AN: 151940 Hom.: 4423 Cov.: 32

Gnomad AFR AF: 0.223

Gnomad AMI AF: 0.164

Gnomad AMR AF: 0.248

Gnomad ASJ AF: 0.233

Gnomad EAS AF: 0.320

Gnomad SAS AF: 0.154

Gnomad FIN AF: 0.210

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.249

Gnomad OTH AF: 0.266

GnomAD4 exome AF: 0.235 AC: 8 AN: 34 Hom.: 2 Cov.: 0 AF XY: 0.231 AC XY: 6 AN XY: 26

Gnomad4 EAS exome AF: 1.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 NFE exome AF: 0.179

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.238 AC: 36173 AN: 152058 Hom.: 4432 Cov.: 32 AF XY: 0.235 AC XY: 17480 AN XY: 74342

Gnomad4 AFR AF: 0.223

Gnomad4 AMR AF: 0.248

Gnomad4 ASJ AF: 0.233

Gnomad4 EAS AF: 0.320

Gnomad4 SAS AF: 0.154

Gnomad4 FIN AF: 0.210

Gnomad4 NFE AF: 0.249

Gnomad4 OTH AF: 0.270

Alfa AF: 0.243 Hom.: 4912

Bravo AF: 0.245

Asia WGS AF: 0.231 AC: 803 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	6.2
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3915971; hg19: chr6-31269348;