chr1-72299433-G-A

Variant names:

• chr1-72299433-G-A
• rs2568958
• ENST00000715640.2:n.236+16028G>A

Variant summary

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

The ENST00000715640.2(LINC02796):​n.236+16028G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.625 in 151,952 control chromosomes in the GnomAD database, including 30,286 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 0.62 (30286 hom., cov: 31)
• Consequence: LINC02796 ENST00000715640.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.388
• Publications: 152 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=-0.95).
• 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

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
	LINC02796	ENST00000715640.2		n.236+16028G>A		intron	N/A
	LINC02796	ENST00000715641.1		n.227+16028G>A		intron	N/A
	LINC02796	ENST00000715642.1		n.153+16028G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.625 AC: 94872 AN: 151834 Hom.: 30272 Cov.: 31

Gnomad AFR AF: 0.541

Gnomad AMI AF: 0.554

Gnomad AMR AF: 0.708

Gnomad ASJ AF: 0.735

Gnomad EAS AF: 0.924

Gnomad SAS AF: 0.667

Gnomad FIN AF: 0.648

Gnomad MID AF: 0.722

Gnomad NFE AF: 0.623

Gnomad OTH AF: 0.640

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

GnomAD4 genome AF: 0.625 AC: 94918 AN: 151952 Hom.: 30286 Cov.: 31 AF XY: 0.631 AC XY: 46868 AN XY: 74288

African (AFR) AF: 0.540 AC: 22364 AN: 41424

American (AMR) AF: 0.708 AC: 10813 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.735 AC: 2550 AN: 3468

East Asian (EAS) AF: 0.923 AC: 4724 AN: 5118

South Asian (SAS) AF: 0.668 AC: 3218 AN: 4816

European-Finnish (FIN) AF: 0.648 AC: 6856 AN: 10576

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

European-Non Finnish (NFE) AF: 0.623 AC: 42317 AN: 67966

Other (OTH) AF: 0.643 AC: 1357 AN: 2110

Alfa AF: 0.631 Hom.: 131084

Bravo AF: 0.628

Asia WGS AF: 0.753 AC: 2614 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.14
DANN	Benign	0.31
PhyloP100		-0.39

Splicing

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

Other links and lift over

dbSNP: rs2568958; hg19: chr1-72765116;