rs7531118

Variant names:

• chr1-72371556-T-C
• rs7531118
• ENST00000715640.2:n.236+88151T>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+88151T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.402 in 152,118 control chromosomes in the GnomAD database, including 15,213 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 0.40 (15213 hom., cov: 32)
• Consequence: LINC02796 ENST00000715640.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.206
• Publications: 62 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=-0.71).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.54 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+88151T>C		intron	N/A
	LINC02796	ENST00000715641.1		n.227+88151T>C		intron	N/A
	LINC02796	ENST00000715642.1		n.153+88151T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.402 AC: 61089 AN: 152000 Hom.: 15214 Cov.: 32

Gnomad AFR AF: 0.112

Gnomad AMI AF: 0.453

Gnomad AMR AF: 0.436

Gnomad ASJ AF: 0.591

Gnomad EAS AF: 0.270

Gnomad SAS AF: 0.327

Gnomad FIN AF: 0.593

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.545

Gnomad OTH AF: 0.423

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

GnomAD4 genome AF: 0.402 AC: 61095 AN: 152118 Hom.: 15213 Cov.: 32 AF XY: 0.404 AC XY: 30029 AN XY: 74350

African (AFR) AF: 0.112 AC: 4647 AN: 41548

American (AMR) AF: 0.436 AC: 6651 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.591 AC: 2051 AN: 3468

East Asian (EAS) AF: 0.271 AC: 1396 AN: 5154

South Asian (SAS) AF: 0.328 AC: 1581 AN: 4816

European-Finnish (FIN) AF: 0.593 AC: 6276 AN: 10580

Middle Eastern (MID) AF: 0.463 AC: 136 AN: 294

European-Non Finnish (NFE) AF: 0.545 AC: 37053 AN: 67976

Other (OTH) AF: 0.424 AC: 892 AN: 2104

Alfa AF: 0.491 Hom.: 64684

Bravo AF: 0.380

Asia WGS AF: 0.278 AC: 966 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	9.7
DANN	Benign	0.89
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs7531118; hg19: chr1-72837239;