rs2853924

Positions:

• chr6-31297369-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.2268T>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 0.104 in 152,288 control chromosomes in the GnomAD database, including 910 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 0.10 (910 hom., cov: 33)
• Consequence: LOC112267902 XR_926691.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.330

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=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.122 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC112267902	XR_926691.3	n.2268T>A		non_coding_transcript_exon_variant	5/5
LINC02571	NR_149115.1	n.167-2356T>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02571	ENST00000539514.1	n.172-2356T>A		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.104 AC: 15829 AN: 152170 Hom.: 911 Cov.: 33

Gnomad AFR AF: 0.0780

Gnomad AMI AF: 0.127

Gnomad AMR AF: 0.115

Gnomad ASJ AF: 0.150

Gnomad EAS AF: 0.114

Gnomad SAS AF: 0.0741

Gnomad FIN AF: 0.0524

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.124

Gnomad OTH AF: 0.115

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

GnomAD4 genome AF: 0.104 AC: 15829 AN: 152288 Hom.: 910 Cov.: 33 AF XY: 0.0988 AC XY: 7358 AN XY: 74474

Gnomad4 AFR AF: 0.0778

Gnomad4 AMR AF: 0.115

Gnomad4 ASJ AF: 0.150

Gnomad4 EAS AF: 0.114

Gnomad4 SAS AF: 0.0738

Gnomad4 FIN AF: 0.0524

Gnomad4 NFE AF: 0.124

Gnomad4 OTH AF: 0.116

Alfa AF: 0.109 Hom.: 138

Bravo AF: 0.109

Asia WGS AF: 0.115 AC: 400 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	7.7
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2853924; hg19: chr6-31265146;