chr11-133799492-G-A

Position:

• chr11-133799492-G-A

Variant summary

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

The NR_120444.1(LINC02743):​n.121+10585C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.103 in 152,180 control chromosomes in the GnomAD database, including 945 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 0.10 (945 hom., cov: 33)
• Consequence: LINC02743 NR_120444.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.276

Genes affected

LINC02743 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.22 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC02743	NR_120444.1	n.121+10585C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02743	ENST00000526254.1	n.121+10585C>T		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.103 AC: 15655 AN: 152062 Hom.: 942 Cov.: 33

Gnomad AFR AF: 0.124

Gnomad AMI AF: 0.0866

Gnomad AMR AF: 0.100

Gnomad ASJ AF: 0.0842

Gnomad EAS AF: 0.231

Gnomad SAS AF: 0.134

Gnomad FIN AF: 0.0529

Gnomad MID AF: 0.134

Gnomad NFE AF: 0.0872

Gnomad OTH AF: 0.109

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

GnomAD4 genome AF: 0.103 AC: 15680 AN: 152180 Hom.: 945 Cov.: 33 AF XY: 0.102 AC XY: 7583 AN XY: 74396

Gnomad4 AFR AF: 0.125

Gnomad4 AMR AF: 0.100

Gnomad4 ASJ AF: 0.0842

Gnomad4 EAS AF: 0.231

Gnomad4 SAS AF: 0.134

Gnomad4 FIN AF: 0.0529

Gnomad4 NFE AF: 0.0872

Gnomad4 OTH AF: 0.108

Alfa AF: 0.0934 Hom.: 1496

Bravo AF: 0.108

Asia WGS AF: 0.185 AC: 645 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	3.4
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2723603; hg19: chr11-133669387;