ENST00000715640.2:n.236+62816G>T

Variant names:

• chr1-72346221-G-T
• rs11209948
• ENST00000715640.2:n.236+62816G>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+62816G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.637 in 151,856 control chromosomes in the GnomAD database, including 31,342 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 0.64 (31342 hom., cov: 31)
• Consequence: LINC02796 ENST00000715640.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.223
• Publications: 27 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=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.901 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02796	ENST00000715640.2		n.236+62816G>T		intron	N/A
	LINC02796	ENST00000715641.1		n.227+62816G>T		intron	N/A
	LINC02796	ENST00000715642.1		n.153+62816G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.637 AC: 96702 AN: 151738 Hom.: 31325 Cov.: 31

Gnomad AFR AF: 0.584

Gnomad AMI AF: 0.556

Gnomad AMR AF: 0.710

Gnomad ASJ AF: 0.736

Gnomad EAS AF: 0.924

Gnomad SAS AF: 0.667

Gnomad FIN AF: 0.649

Gnomad MID AF: 0.722

Gnomad NFE AF: 0.623

Gnomad OTH AF: 0.650

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

GnomAD4 genome AF: 0.637 AC: 96757 AN: 151856 Hom.: 31342 Cov.: 31 AF XY: 0.643 AC XY: 47730 AN XY: 74224

African (AFR) AF: 0.584 AC: 24168 AN: 41414

American (AMR) AF: 0.711 AC: 10848 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.736 AC: 2549 AN: 3464

East Asian (EAS) AF: 0.923 AC: 4751 AN: 5148

South Asian (SAS) AF: 0.668 AC: 3214 AN: 4812

European-Finnish (FIN) AF: 0.649 AC: 6852 AN: 10564

Middle Eastern (MID) AF: 0.731 AC: 215 AN: 294

European-Non Finnish (NFE) AF: 0.623 AC: 42279 AN: 67888

Other (OTH) AF: 0.653 AC: 1375 AN: 2106

Alfa AF: 0.586 Hom.: 5721

Bravo AF: 0.642

Asia WGS AF: 0.758 AC: 2632 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.68
DANN	Benign	0.49
PhyloP100		-0.22

Splicing

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

Other links and lift over

dbSNP: rs11209948; hg19: chr1-72811904;