rs9366778

Variant names:

• chr6-31301396-G-A
• rs9366778
• ENST00000539514.1:n.171+76C>T

Variant summary

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

The ENST00000539514.1(LINC02571):​n.171+76C>T 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 150,880 control chromosomes in the GnomAD database, including 17,537 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 (17536 hom., cov: 31)
  • Exomes 𝑓: 0.40 (1 hom.)
• Consequence: LINC02571 ENST00000539514.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.913
• Publications: 39 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=-1.01).
• 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02571	NR_149115.1		n.166+76C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02571	ENST00000539514.1	TSL:4	n.171+76C>T		intron	N/A
	ENSG00000298396	ENST00000755297.1		n.32+30290G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.473 AC: 71321 AN: 150752 Hom.: 17513 Cov.: 31

Gnomad AFR AF: 0.533

Gnomad AMI AF: 0.320

Gnomad AMR AF: 0.549

Gnomad ASJ AF: 0.396

Gnomad EAS AF: 0.617

Gnomad SAS AF: 0.609

Gnomad FIN AF: 0.516

Gnomad MID AF: 0.564

Gnomad NFE AF: 0.398

Gnomad OTH AF: 0.493

GnomAD4 exome AF: 0.400 AC: 4 AN: 10 Hom.: 1 AF XY: 0.400 AC XY: 4 AN XY: 10

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.375 AC: 3 AN: 8

Other (OTH) AF: 0.500 AC: 1 AN: 2

GnomAD4 genome AF: 0.473 AC: 71395 AN: 150870 Hom.: 17536 Cov.: 31 AF XY: 0.483 AC XY: 35596 AN XY: 73700

African (AFR) AF: 0.532 AC: 21860 AN: 41062

American (AMR) AF: 0.550 AC: 8355 AN: 15196

Ashkenazi Jewish (ASJ) AF: 0.396 AC: 1359 AN: 3434

East Asian (EAS) AF: 0.618 AC: 3172 AN: 5134

South Asian (SAS) AF: 0.609 AC: 2917 AN: 4788

European-Finnish (FIN) AF: 0.516 AC: 5390 AN: 10454

Middle Eastern (MID) AF: 0.579 AC: 169 AN: 292

European-Non Finnish (NFE) AF: 0.398 AC: 26847 AN: 67510

Other (OTH) AF: 0.494 AC: 1039 AN: 2104

Alfa AF: 0.435 Hom.: 34146

Bravo AF: 0.477

Asia WGS AF: 0.618 AC: 2149 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	7.1
DANN	Benign	0.29
PhyloP100		-0.91

Splicing

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

Other links and lift over

dbSNP: rs9366778; hg19: chr6-31269173;