chr11-96717198-G-T

Variant names:

• chr11-96717198-G-T
• rs3018626
• ENST00000716805.1:n.389+56299G>T

Variant summary

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

The ENST00000716805.1(LINC02737):​n.389+56299G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.195 in 152,172 control chromosomes in the GnomAD database, including 3,166 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 0.19 (3166 hom., cov: 33)
• Consequence: LINC02737 ENST00000716805.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.661
• Publications: 3 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 (SAS) allele frequency at 95% confidence interval = 0.282 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

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	ENST00000716805.1		n.389+56299G>T		intron	N/A
	LINC02737	ENST00000716807.1		n.618+56299G>T		intron	N/A
	LINC02737	ENST00000716809.1		n.146-51391G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.195 AC: 29637 AN: 152054 Hom.: 3161 Cov.: 33

Gnomad AFR AF: 0.0982

Gnomad AMI AF: 0.198

Gnomad AMR AF: 0.194

Gnomad ASJ AF: 0.250

Gnomad EAS AF: 0.171

Gnomad SAS AF: 0.292

Gnomad FIN AF: 0.206

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.243

Gnomad OTH AF: 0.212

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

GnomAD4 genome AF: 0.195 AC: 29652 AN: 152172 Hom.: 3166 Cov.: 33 AF XY: 0.194 AC XY: 14432 AN XY: 74394

African (AFR) AF: 0.0981 AC: 4075 AN: 41552

American (AMR) AF: 0.194 AC: 2964 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.250 AC: 868 AN: 3470

East Asian (EAS) AF: 0.170 AC: 881 AN: 5184

South Asian (SAS) AF: 0.294 AC: 1420 AN: 4824

European-Finnish (FIN) AF: 0.206 AC: 2180 AN: 10578

Middle Eastern (MID) AF: 0.262 AC: 77 AN: 294

European-Non Finnish (NFE) AF: 0.243 AC: 16546 AN: 67978

Other (OTH) AF: 0.218 AC: 460 AN: 2108

Alfa AF: 0.227 Hom.: 2841

Bravo AF: 0.182

Asia WGS AF: 0.249 AC: 864 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.0
DANN	Benign	0.53
PhyloP100		-0.66

Splicing

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

Other links and lift over

dbSNP: rs3018626; hg19: chr11-96588198;