rs10789336

Variant names:

• chr1-72372723-G-A
• rs10789336
• ENST00000715640.2:n.236+89318G>A

Your query was ambiguous. Multiple possible variants found:

• chr1-72372723-G-A
• chr1-72372723-G-C

Variant summary

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

The ENST00000715640.2(LINC02796):​n.236+89318G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.62 in 151,982 control chromosomes in the GnomAD database, including 29,816 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 (29816 hom., cov: 31)
• Consequence: LINC02796 ENST00000715640.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.147
• Publications: 32 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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.897 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+89318G>A		intron	N/A
	LINC02796	ENST00000715641.1		n.227+89318G>A		intron	N/A
	LINC02796	ENST00000715642.1		n.153+89318G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.620 AC: 94149 AN: 151864 Hom.: 29802 Cov.: 31

Gnomad AFR AF: 0.531

Gnomad AMI AF: 0.555

Gnomad AMR AF: 0.704

Gnomad ASJ AF: 0.737

Gnomad EAS AF: 0.920

Gnomad SAS AF: 0.664

Gnomad FIN AF: 0.652

Gnomad MID AF: 0.741

Gnomad NFE AF: 0.618

Gnomad OTH AF: 0.643

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

GnomAD4 genome AF: 0.620 AC: 94197 AN: 151982 Hom.: 29816 Cov.: 31 AF XY: 0.627 AC XY: 46569 AN XY: 74276

African (AFR) AF: 0.530 AC: 21955 AN: 41416

American (AMR) AF: 0.704 AC: 10760 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.737 AC: 2558 AN: 3470

East Asian (EAS) AF: 0.919 AC: 4741 AN: 5158

South Asian (SAS) AF: 0.665 AC: 3205 AN: 4818

European-Finnish (FIN) AF: 0.652 AC: 6902 AN: 10578

Middle Eastern (MID) AF: 0.745 AC: 219 AN: 294

European-Non Finnish (NFE) AF: 0.618 AC: 41989 AN: 67956

Other (OTH) AF: 0.647 AC: 1362 AN: 2106

Alfa AF: 0.586 Hom.: 5941

Bravo AF: 0.623

Asia WGS AF: 0.751 AC: 2607 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.1
DANN	Benign	0.46
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs10789336; hg19: chr1-72838406;