chr1-72346757-G-A

Variant names:

• chr1-72346757-G-A
• rs2815752
• ENST00000715640.2:n.236+63352G>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+63352G>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 151,932 control chromosomes in the GnomAD database, including 30,302 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 (30302 hom., cov: 31)
• Consequence: LINC02796 ENST00000715640.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0410
• Publications: 224 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=-0.83).
• 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+63352G>A		intron	N/A
	LINC02796	ENST00000715641.1		n.227+63352G>A		intron	N/A
	LINC02796	ENST00000715642.1		n.153+63352G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.625 AC: 94889 AN: 151814 Hom.: 30286 Cov.: 31

Gnomad AFR AF: 0.541

Gnomad AMI AF: 0.555

Gnomad AMR AF: 0.707

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: 0.639

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

GnomAD4 genome AF: 0.625 AC: 94939 AN: 151932 Hom.: 30302 Cov.: 31 AF XY: 0.631 AC XY: 46861 AN XY: 74240

African (AFR) AF: 0.540 AC: 22378 AN: 41416

American (AMR) AF: 0.708 AC: 10809 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.736 AC: 2554 AN: 3472

East Asian (EAS) AF: 0.923 AC: 4764 AN: 5162

South Asian (SAS) AF: 0.668 AC: 3212 AN: 4808

European-Finnish (FIN) AF: 0.649 AC: 6847 AN: 10558

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

European-Non Finnish (NFE) AF: 0.623 AC: 42304 AN: 67938

Other (OTH) AF: 0.642 AC: 1350 AN: 2102

Alfa AF: 0.634 Hom.: 139379

Bravo AF: 0.628

Asia WGS AF: 0.753 AC: 2614 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.8
DANN	Benign	0.78
PhyloP100		0.041

Splicing

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

Other links and lift over

dbSNP: rs2815752; hg19: chr1-72812440;