rs773506

Variant names:

• chr9-91213189-G-A
• rs773506
• ENST00000667274.1:n.-143C>T

Your query was ambiguous. Multiple possible variants found:

• chr9-91213189-G-A
• chr9-91213189-G-C
• chr9-91213189-G-T

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02937	ENST00000667274.1	n.-143C>T		upstream_gene_variant

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

Gnomad4 AFR AF: 0.231

Gnomad4 AMR AF: 0.642

Gnomad4 ASJ AF: 0.505

Gnomad4 EAS AF: 0.295

Gnomad4 SAS AF: 0.526

Gnomad4 FIN AF: 0.574

Gnomad4 NFE AF: 0.643

Gnomad4 OTH AF: 0.529

Alfa AF: 0.607 Hom.: 47397

Bravo AF: 0.493

Asia WGS AF: 0.392 AC: 1361 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	0.92
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs773506; hg19: chr9-93975471;