1-72358030-C-T

Variant names:

• chr1-72358030-C-T
• rs990871
• ENST00000715640.2:n.236+74625C>T

Variant summary

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

The ENST00000715640.2(LINC02796):​n.236+74625C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.591 in 151,940 control chromosomes in the GnomAD database, including 27,713 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 0.59 (27713 hom., cov: 32)
• Consequence: LINC02796 ENST00000715640.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.839
• Publications: 21 publications found

Genes affected

LINC02796 (HGNC:27918): (long intergenic non-protein coding RNA 2796)

LOC105378797 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.898 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000715640.2. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02796	ENST00000715640.2		n.236+74625C>T		intron	N/A
	LINC02796	ENST00000715641.1		n.227+74625C>T		intron	N/A
	LINC02796	ENST00000715642.1		n.153+74625C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.592 AC: 89813 AN: 151822 Hom.: 27705 Cov.: 32

Gnomad AFR AF: 0.432

Gnomad AMI AF: 0.555

Gnomad AMR AF: 0.694

Gnomad ASJ AF: 0.737

Gnomad EAS AF: 0.921

Gnomad SAS AF: 0.663

Gnomad FIN AF: 0.652

Gnomad MID AF: 0.722

Gnomad NFE AF: 0.618

Gnomad OTH AF: 0.623

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

GnomAD4 genome AF: 0.591 AC: 89839 AN: 151940 Hom.: 27713 Cov.: 32 AF XY: 0.599 AC XY: 44501 AN XY: 74286

African (AFR) AF: 0.431 AC: 17843 AN: 41412

American (AMR) AF: 0.694 AC: 10604 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.737 AC: 2560 AN: 3472

East Asian (EAS) AF: 0.920 AC: 4746 AN: 5158

South Asian (SAS) AF: 0.664 AC: 3196 AN: 4810

European-Finnish (FIN) AF: 0.652 AC: 6882 AN: 10552

Middle Eastern (MID) AF: 0.724 AC: 213 AN: 294

European-Non Finnish (NFE) AF: 0.618 AC: 41970 AN: 67954

Other (OTH) AF: 0.626 AC: 1319 AN: 2106

Alfa AF: 0.616 Hom.: 85041

Bravo AF: 0.590

Asia WGS AF: 0.742 AC: 2572 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.88
DANN	Benign	0.72
PhyloP100		-0.84

Splicing

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

Other links and lift over

dbSNP: rs990871; hg19: chr1-72823713;