rs1944511

Positions:

• chr11-119992875-G-A
• chr11-119992875-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_183635.1(LINC02744):​n.137+1719C>T variant causes a intron, non coding transcript 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 NR_183635.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.03

Genes affected

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

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02744	NR_183635.1	n.137+1719C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02744	ENST00000662076.1	n.116+1719C>T		intron_variant, non_coding_transcript_variant
	ENST00000701821.1	n.408+16723G>A		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.280

Gnomad4 AMR AF: 0.168

Gnomad4 ASJ AF: 0.287

Gnomad4 EAS AF: 0.0143

Gnomad4 SAS AF: 0.257

Gnomad4 FIN AF: 0.282

Gnomad4 NFE AF: 0.242

Gnomad4 OTH AF: 0.237

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1944511; hg19: chr11-119863584;