chr5-979033-C-T

Variant names:

• chr5-979033-C-T
• rs2289827
• ENST00000511936.2:n.207C>T

Variant summary

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

The ENST00000511936.2(ENSG00000250173):​n.207C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.772 in 152,018 control chromosomes in the GnomAD database, including 45,437 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 0.77 (45437 hom., cov: 31)
• Consequence: ENSG00000250173 ENST00000511936.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.662
• Publications: 2 publications found

Genes affected

ENSG00000250173 (HGNC:):

LINC02982 (HGNC:56056): (long intergenic non-protein coding RNA 2982)

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 (AMR) allele frequency at 95% confidence interval = 0.81 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
ENSG00000250173	ENST00000511936.2	n.207C>T		non_coding_transcript_exon_variant	Exon 2 of 3	2
ENSG00000250173	ENST00000804475.1	n.325C>T		non_coding_transcript_exon_variant	Exon 1 of 2
LINC02982	ENST00000804386.1	n.77-13068G>A		intron_variant	Intron 1 of 1
ENSG00000250173	ENST00000804471.1	n.323-2003C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.772 AC: 117264 AN: 151900 Hom.: 45395 Cov.: 31

Gnomad AFR AF: 0.787

Gnomad AMI AF: 0.641

Gnomad AMR AF: 0.822

Gnomad ASJ AF: 0.820

Gnomad EAS AF: 0.713

Gnomad SAS AF: 0.775

Gnomad FIN AF: 0.691

Gnomad MID AF: 0.759

Gnomad NFE AF: 0.768

Gnomad OTH AF: 0.778

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

GnomAD4 genome AF: 0.772 AC: 117368 AN: 152018 Hom.: 45437 Cov.: 31 AF XY: 0.770 AC XY: 57176 AN XY: 74272

African (AFR) AF: 0.787 AC: 32600 AN: 41448

American (AMR) AF: 0.822 AC: 12570 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.820 AC: 2845 AN: 3468

East Asian (EAS) AF: 0.713 AC: 3680 AN: 5164

South Asian (SAS) AF: 0.776 AC: 3742 AN: 4822

European-Finnish (FIN) AF: 0.691 AC: 7285 AN: 10542

Middle Eastern (MID) AF: 0.755 AC: 222 AN: 294

European-Non Finnish (NFE) AF: 0.768 AC: 52200 AN: 67976

Other (OTH) AF: 0.779 AC: 1641 AN: 2106

Alfa AF: 0.772 Hom.: 67933

Bravo AF: 0.782

Asia WGS AF: 0.738 AC: 2567 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.5
DANN	Benign	0.53
PhyloP100		-0.66

Splicing

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

Other links and lift over

dbSNP: rs2289827; hg19: chr5-979148;