6-31298745-G-T

Variant names:

• chr6-31298745-G-T
• rs2524089
• ENST00000539514.1:n.171+2727C>A

Variant summary

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

The ENST00000539514.1(LINC02571):​n.171+2727C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.649 in 151,800 control chromosomes in the GnomAD database, including 32,215 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 (32215 hom., cov: 30)
• Consequence: LINC02571 ENST00000539514.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01
• Publications: 46 publications found

Genes affected

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

ENSG00000298396 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.718 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02571	NR_149115.1	n.166+2727C>A		intron_variant	Intron 1 of 3
LOC112267902	XR_926691.3	n.1061-169C>A		intron_variant	Intron 4 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02571	ENST00000539514.1	n.171+2727C>A		intron_variant	Intron 1 of 3	4
ENSG00000298396	ENST00000755297.1	n.32+27639G>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.649 AC: 98411 AN: 151682 Hom.: 32173 Cov.: 30

Gnomad AFR AF: 0.699

Gnomad AMI AF: 0.480

Gnomad AMR AF: 0.713

Gnomad ASJ AF: 0.583

Gnomad EAS AF: 0.736

Gnomad SAS AF: 0.700

Gnomad FIN AF: 0.669

Gnomad MID AF: 0.656

Gnomad NFE AF: 0.595

Gnomad OTH AF: 0.678

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

GnomAD4 genome AF: 0.649 AC: 98505 AN: 151800 Hom.: 32215 Cov.: 30 AF XY: 0.653 AC XY: 48471 AN XY: 74172

African (AFR) AF: 0.699 AC: 28955 AN: 41406

American (AMR) AF: 0.714 AC: 10881 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.583 AC: 2020 AN: 3466

East Asian (EAS) AF: 0.737 AC: 3799 AN: 5152

South Asian (SAS) AF: 0.700 AC: 3357 AN: 4798

European-Finnish (FIN) AF: 0.669 AC: 7032 AN: 10514

Middle Eastern (MID) AF: 0.668 AC: 195 AN: 292

European-Non Finnish (NFE) AF: 0.595 AC: 40399 AN: 67910

Other (OTH) AF: 0.679 AC: 1429 AN: 2106

Alfa AF: 0.614 Hom.: 125090

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	-0.92
CADD	Benign	4.8
DANN	Benign	0.64
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs2524089; hg19: chr6-31266522;