ENST00000716805.1:n.124-59856A>C

Variant names:

• chr11-96599737-A-C
• rs10501861
• ENST00000716805.1:n.124-59856A>C

Variant summary

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

The ENST00000716805.1(LINC02737):​n.124-59856A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.014 in 152,078 control chromosomes in the GnomAD database, including 53 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 0.014 (53 hom., cov: 31)
• Consequence: LINC02737 ENST00000716805.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.147
• Publications: 0 publications found

Genes affected

LINC02737 (HGNC:54254): (long intergenic non-protein coding RNA 2737)

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 = 0.0521 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000716805.1. 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
	LINC02737	ENST00000716805.1		n.124-59856A>C		intron	N/A
	LINC02737	ENST00000716807.1		n.352+11504A>C		intron	N/A
	LINC02737	ENST00000716808.1		n.158+9263A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0140 AC: 2128 AN: 151960 Hom.: 51 Cov.: 31

Gnomad AFR AF: 0.00940

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.0471

Gnomad ASJ AF: 0.00519

Gnomad EAS AF: 0.0579

Gnomad SAS AF: 0.0263

Gnomad FIN AF: 0.0101

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.00632

Gnomad OTH AF: 0.0163

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

GnomAD4 genome AF: 0.0140 AC: 2135 AN: 152078 Hom.: 53 Cov.: 31 AF XY: 0.0149 AC XY: 1109 AN XY: 74332

African (AFR) AF: 0.00954 AC: 396 AN: 41498

American (AMR) AF: 0.0476 AC: 726 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.00519 AC: 18 AN: 3470

East Asian (EAS) AF: 0.0575 AC: 296 AN: 5152

South Asian (SAS) AF: 0.0253 AC: 122 AN: 4826

European-Finnish (FIN) AF: 0.0101 AC: 107 AN: 10574

Middle Eastern (MID) AF: 0.0102 AC: 3 AN: 294

European-Non Finnish (NFE) AF: 0.00632 AC: 430 AN: 67986

Other (OTH) AF: 0.0161 AC: 34 AN: 2110

Alfa AF: 0.00942 Hom.: 1

Bravo AF: 0.0170

Asia WGS AF: 0.0460 AC: 161 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	6.5
DANN	Benign	0.72
PhyloP100		0.15

Splicing

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

Other links and lift over

dbSNP: rs10501861; hg19: chr11-96470737;