chr11-119992875-G-A

Variant names:

• chr11-119992875-G-A
• rs1944511
• ENST00000524708.1:n.150+2013C>T

Variant summary

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

The ENST00000534055.2(LINC02744):​n.110+1719C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.241 in 151,952 control chromosomes in the GnomAD database, including 4,569 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 0.24 (4569 hom., cov: 33)
• Consequence: LINC02744 ENST00000534055.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.03
• Publications: 4 publications found

Genes affected

LINC02744 (HGNC:54262): (long intergenic non-protein coding RNA 2744)

ENSG00000286992 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.276 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000534055.2. 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
	LINC02744	NR_183635.1		n.137+1719C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02744	ENST00000524708.1	TSL:3	n.150+2013C>T		intron	N/A
	LINC02744	ENST00000526934.1	TSL:3	n.116+1719C>T		intron	N/A
	LINC02744	ENST00000534055.2	TSL:2	n.110+1719C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.241 AC: 36573 AN: 151834 Hom.: 4571 Cov.: 33

Gnomad AFR AF: 0.280

Gnomad AMI AF: 0.174

Gnomad AMR AF: 0.168

Gnomad ASJ AF: 0.287

Gnomad EAS AF: 0.0145

Gnomad SAS AF: 0.258

Gnomad FIN AF: 0.282

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.242

Gnomad OTH AF: 0.240

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

GnomAD4 genome AF: 0.241 AC: 36584 AN: 151952 Hom.: 4569 Cov.: 33 AF XY: 0.239 AC XY: 17759 AN XY: 74284

African (AFR) AF: 0.280 AC: 11571 AN: 41324

American (AMR) AF: 0.168 AC: 2562 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.287 AC: 997 AN: 3468

East Asian (EAS) AF: 0.0143 AC: 74 AN: 5168

South Asian (SAS) AF: 0.257 AC: 1238 AN: 4818

European-Finnish (FIN) AF: 0.282 AC: 2982 AN: 10592

Middle Eastern (MID) AF: 0.245 AC: 72 AN: 294

European-Non Finnish (NFE) AF: 0.242 AC: 16430 AN: 67980

Other (OTH) AF: 0.237 AC: 500 AN: 2112

Alfa AF: 0.123 Hom.: 199

Bravo AF: 0.231

Asia WGS AF: 0.133 AC: 462 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.054
DANN	Benign	0.52
PhyloP100		-4.0

Splicing

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

Other links and lift over

dbSNP: rs1944511; hg19: chr11-119863584;