rs9380240

Variant names:

• chr6-31301055-T-C
• rs9380240
• ENST00000539514.1:n.171+417A>G

Variant summary

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

The ENST00000539514.1(LINC02571):​n.171+417A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.473 in 151,850 control chromosomes in the GnomAD database, including 17,487 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 0.47 (17487 hom., cov: 31)
• Consequence: LINC02571 ENST00000539514.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.44
• Publications: 17 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=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.6 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.166+417A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02571	ENST00000539514.1	TSL:4	n.171+417A>G		intron	N/A
	ENSG00000298396	ENST00000755297.1		n.32+29949T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.473 AC: 71803 AN: 151732 Hom.: 17464 Cov.: 31

Gnomad AFR AF: 0.533

Gnomad AMI AF: 0.325

Gnomad AMR AF: 0.550

Gnomad ASJ AF: 0.397

Gnomad EAS AF: 0.617

Gnomad SAS AF: 0.608

Gnomad FIN AF: 0.515

Gnomad MID AF: 0.560

Gnomad NFE AF: 0.398

Gnomad OTH AF: 0.496

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

GnomAD4 genome AF: 0.473 AC: 71878 AN: 151850 Hom.: 17487 Cov.: 31 AF XY: 0.484 AC XY: 35886 AN XY: 74220

African (AFR) AF: 0.533 AC: 22049 AN: 41384

American (AMR) AF: 0.550 AC: 8395 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.397 AC: 1376 AN: 3468

East Asian (EAS) AF: 0.618 AC: 3193 AN: 5164

South Asian (SAS) AF: 0.608 AC: 2929 AN: 4816

European-Finnish (FIN) AF: 0.515 AC: 5417 AN: 10522

Middle Eastern (MID) AF: 0.575 AC: 169 AN: 294

European-Non Finnish (NFE) AF: 0.398 AC: 27007 AN: 67918

Other (OTH) AF: 0.497 AC: 1047 AN: 2108

Alfa AF: 0.424 Hom.: 37326

Bravo AF: 0.477

Asia WGS AF: 0.618 AC: 2148 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	3.2
DANN	Benign	0.35
PhyloP100		-2.4

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs9380240;

hg19: chr6-31268832;