rs2524095

Positions:

• chr6-31298340-A-C
• chr6-31298340-A-T

Variant summary

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

The XR_926691.3(LOC112267902):​n.1297T>G 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 0.649 in 152,036 control chromosomes in the GnomAD database, including 32,259 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 0.65 (32259 hom., cov: 31)
• Consequence: LOC112267902 XR_926691.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.362

Genes affected

LOC112267902 (HGNC:):

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.716 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC112267902	XR_926691.3	n.1297T>G		non_coding_transcript_exon_variant	5/5
LINC02571	NR_149115.1	n.166+3132T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02571	ENST00000539514.1	n.171+3132T>G		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.649 AC: 98544 AN: 151916 Hom.: 32217 Cov.: 31

Gnomad AFR AF: 0.699

Gnomad AMI AF: 0.481

Gnomad AMR AF: 0.713

Gnomad ASJ AF: 0.582

Gnomad EAS AF: 0.735

Gnomad SAS AF: 0.701

Gnomad FIN AF: 0.669

Gnomad MID AF: 0.650

Gnomad NFE AF: 0.595

Gnomad OTH AF: 0.679

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

GnomAD4 genome AF: 0.649 AC: 98639 AN: 152036 Hom.: 32259 Cov.: 31 AF XY: 0.653 AC XY: 48550 AN XY: 74306

Gnomad4 AFR AF: 0.699

Gnomad4 AMR AF: 0.714

Gnomad4 ASJ AF: 0.582

Gnomad4 EAS AF: 0.736

Gnomad4 SAS AF: 0.701

Gnomad4 FIN AF: 0.669

Gnomad4 NFE AF: 0.595

Gnomad4 OTH AF: 0.679

Alfa AF: 0.615 Hom.: 13664

Bravo AF: 0.656

Asia WGS AF: 0.751 AC: 2609 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	5.1
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2524095; hg19: chr6-31266117;