ENST00000667274.1:n.-143C>T

Variant names:

• chr9-91213189-G-A
• rs773506
• ENST00000815380.1:n.149+2565G>A

Variant summary

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

The ENST00000667274.1(LINC02937):​n.-143C>T variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.505 in 152,040 control chromosomes in the GnomAD database, including 22,006 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 (22006 hom., cov: 31)
• Consequence: LINC02937 ENST00000667274.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.156
• Publications: 31 publications found

Genes affected

ENSG00000306114 (HGNC:):

LINC02937 (HGNC:55942): (long intergenic non-protein coding RNA 2937)

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 (NFE) allele frequency at 95% confidence interval = 0.638 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000667274.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000306114	ENST00000815380.1		n.149+2565G>A		intron	N/A
	ENSG00000306114	ENST00000815381.1		n.67-513G>A		intron	N/A
	LINC02937	ENST00000667274.1		n.-143C>T		upstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.505 AC: 76754 AN: 151922 Hom.: 22007 Cov.: 31

Gnomad AFR AF: 0.232

Gnomad AMI AF: 0.611

Gnomad AMR AF: 0.642

Gnomad ASJ AF: 0.505

Gnomad EAS AF: 0.295

Gnomad SAS AF: 0.525

Gnomad FIN AF: 0.574

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.643

Gnomad OTH AF: 0.533

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

GnomAD4 genome AF: 0.505 AC: 76769 AN: 152040 Hom.: 22006 Cov.: 31 AF XY: 0.502 AC XY: 37309 AN XY: 74320

African (AFR) AF: 0.231 AC: 9600 AN: 41480

American (AMR) AF: 0.642 AC: 9812 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.505 AC: 1751 AN: 3470

East Asian (EAS) AF: 0.295 AC: 1526 AN: 5168

South Asian (SAS) AF: 0.526 AC: 2534 AN: 4818

European-Finnish (FIN) AF: 0.574 AC: 6066 AN: 10566

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

European-Non Finnish (NFE) AF: 0.643 AC: 43671 AN: 67950

Other (OTH) AF: 0.529 AC: 1111 AN: 2102

Alfa AF: 0.577 Hom.: 70899

Bravo AF: 0.493

Asia WGS AF: 0.392 AC: 1361 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.92
DANN	Benign	0.55
PhyloP100		0.16

Splicing

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

Other links and lift over

dbSNP: rs773506; hg19: chr9-93975471;