11-42006251-T-C

Position:

• chr11-42006251-T-C

Variant summary

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

The NR_135065.1(LINC02745):​n.1065-167A>G 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 0.145 in 152,094 control chromosomes in the GnomAD database, including 1,650 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 0.14 (1650 hom., cov: 32)
• Consequence: LINC02745 NR_135065.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0620

Genes affected

LINC02745 (HGNC:54263): (long intergenic non-protein coding RNA 2745)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.151 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC02745	NR_135065.1	n.1065-167A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02745	ENST00000527828.6	n.342-12585A>G		intron_variant, non_coding_transcript_variant		3
LINC02745	ENST00000663570.1	n.800-12585A>G		intron_variant, non_coding_transcript_variant
LINC02745	ENST00000667585.1	n.361-12585A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.145 AC: 22029 AN: 151976 Hom.: 1650 Cov.: 32

Gnomad AFR AF: 0.150

Gnomad AMI AF: 0.129

Gnomad AMR AF: 0.107

Gnomad ASJ AF: 0.117

Gnomad EAS AF: 0.141

Gnomad SAS AF: 0.157

Gnomad FIN AF: 0.134

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.154

Gnomad OTH AF: 0.135

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

GnomAD4 genome AF: 0.145 AC: 22051 AN: 152094 Hom.: 1650 Cov.: 32 AF XY: 0.143 AC XY: 10641 AN XY: 74346

Gnomad4 AFR AF: 0.150

Gnomad4 AMR AF: 0.107

Gnomad4 ASJ AF: 0.117

Gnomad4 EAS AF: 0.141

Gnomad4 SAS AF: 0.157

Gnomad4 FIN AF: 0.134

Gnomad4 NFE AF: 0.153

Gnomad4 OTH AF: 0.133

Alfa AF: 0.147 Hom.: 650

Bravo AF: 0.145

Asia WGS AF: 0.158 AC: 546 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.5
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10837766; hg19: chr11-42027801;