XR_926691.3:n.1677T>C

Variant names:

• chr6-31297960-A-G
• rs2853923
• XR_926691.3:n.1677T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_926691.3(LOC112267902):​n.1677T>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 0.498 in 152,056 control chromosomes in the GnomAD database, including 19,058 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 0.50 (19058 hom., cov: 32)
• Consequence: LOC112267902 XR_926691.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.08
• Publications: 17 publications found

Genes affected

LOC112267902 (HGNC:):

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.556 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000539514.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02571	NR_149115.1		n.167-2947T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02571	ENST00000539514.1	TSL:4	n.172-2947T>C		intron	N/A
	ENSG00000298396	ENST00000755297.1		n.32+26854A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.498 AC: 75650 AN: 151938 Hom.: 19044 Cov.: 32

Gnomad AFR AF: 0.518

Gnomad AMI AF: 0.442

Gnomad AMR AF: 0.565

Gnomad ASJ AF: 0.483

Gnomad EAS AF: 0.525

Gnomad SAS AF: 0.549

Gnomad FIN AF: 0.510

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.464

Gnomad OTH AF: 0.512

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

GnomAD4 genome AF: 0.498 AC: 75697 AN: 152056 Hom.: 19058 Cov.: 32 AF XY: 0.500 AC XY: 37125 AN XY: 74318

African (AFR) AF: 0.518 AC: 21466 AN: 41450

American (AMR) AF: 0.566 AC: 8637 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.483 AC: 1675 AN: 3470

East Asian (EAS) AF: 0.526 AC: 2718 AN: 5172

South Asian (SAS) AF: 0.548 AC: 2646 AN: 4826

European-Finnish (FIN) AF: 0.510 AC: 5400 AN: 10578

Middle Eastern (MID) AF: 0.483 AC: 142 AN: 294

European-Non Finnish (NFE) AF: 0.464 AC: 31531 AN: 67978

Other (OTH) AF: 0.511 AC: 1080 AN: 2114

Alfa AF: 0.456 Hom.: 21753

Bravo AF: 0.502

Asia WGS AF: 0.600 AC: 2088 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.0
DANN	Benign	0.35
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs2853923; hg19: chr6-31265737;