1-72372846-A-G

Variant names:

• chr1-72372846-A-G
• rs1993709
• ENST00000715640.2:n.237-89347A>G

Variant summary

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

The ENST00000715640.2(LINC02796):​n.237-89347A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.856 in 152,122 control chromosomes in the GnomAD database, including 55,931 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 0.86 (55931 hom., cov: 31)
• Consequence: LINC02796 ENST00000715640.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.569
• Publications: 36 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 = 0.961 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.237-89347A>G		intron	N/A
	LINC02796	ENST00000715641.1		n.228-89347A>G		intron	N/A
	LINC02796	ENST00000715642.1		n.153+89441A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.856 AC: 130085 AN: 152004 Hom.: 55871 Cov.: 31

Gnomad AFR AF: 0.872

Gnomad AMI AF: 0.789

Gnomad AMR AF: 0.889

Gnomad ASJ AF: 0.892

Gnomad EAS AF: 0.983

Gnomad SAS AF: 0.944

Gnomad FIN AF: 0.867

Gnomad MID AF: 0.858

Gnomad NFE AF: 0.820

Gnomad OTH AF: 0.866

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

GnomAD4 genome AF: 0.856 AC: 130206 AN: 152122 Hom.: 55931 Cov.: 31 AF XY: 0.862 AC XY: 64070 AN XY: 74340

African (AFR) AF: 0.872 AC: 36204 AN: 41528

American (AMR) AF: 0.889 AC: 13569 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.892 AC: 3096 AN: 3472

East Asian (EAS) AF: 0.983 AC: 5090 AN: 5176

South Asian (SAS) AF: 0.945 AC: 4540 AN: 4804

European-Finnish (FIN) AF: 0.867 AC: 9174 AN: 10586

Middle Eastern (MID) AF: 0.864 AC: 254 AN: 294

European-Non Finnish (NFE) AF: 0.820 AC: 55729 AN: 67978

Other (OTH) AF: 0.867 AC: 1832 AN: 2112

Alfa AF: 0.837 Hom.: 126634

Bravo AF: 0.859

Asia WGS AF: 0.962 AC: 3343 AN: 3476

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	0.46
PhyloP100		-0.57

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1993709; hg19: chr1-72838529;