11-96956412-C-G

Variant names:

• chr11-96956412-C-G
• rs651263
• ENST00000716809.1:n.242-19251C>G

Variant summary

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

The ENST00000716809.1(LINC02737):​n.242-19251C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.552 in 151,314 control chromosomes in the GnomAD database, including 23,257 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 0.55 (23257 hom., cov: 33)
• Consequence: LINC02737 ENST00000716809.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.196
• Publications: 1 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.694 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000716809.1. 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
	LINC02737	ENST00000716809.1		n.242-19251C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.552 AC: 83533 AN: 151202 Hom.: 23267 Cov.: 33

Gnomad AFR AF: 0.470

Gnomad AMI AF: 0.468

Gnomad AMR AF: 0.618

Gnomad ASJ AF: 0.532

Gnomad EAS AF: 0.714

Gnomad SAS AF: 0.680

Gnomad FIN AF: 0.612

Gnomad MID AF: 0.593

Gnomad NFE AF: 0.559

Gnomad OTH AF: 0.574

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

GnomAD4 genome AF: 0.552 AC: 83540 AN: 151314 Hom.: 23257 Cov.: 33 AF XY: 0.558 AC XY: 41258 AN XY: 73934

African (AFR) AF: 0.470 AC: 19413 AN: 41324

American (AMR) AF: 0.617 AC: 9389 AN: 15212

Ashkenazi Jewish (ASJ) AF: 0.532 AC: 1837 AN: 3454

East Asian (EAS) AF: 0.713 AC: 3683 AN: 5166

South Asian (SAS) AF: 0.680 AC: 3276 AN: 4820

European-Finnish (FIN) AF: 0.612 AC: 6332 AN: 10342

Middle Eastern (MID) AF: 0.590 AC: 171 AN: 290

European-Non Finnish (NFE) AF: 0.559 AC: 37816 AN: 67694

Other (OTH) AF: 0.570 AC: 1196 AN: 2100

Alfa AF: 0.409 Hom.: 1065

Bravo AF: 0.547

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.3
DANN	Benign	0.63
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs651263; hg19: chr11-96827412;