rs2403456

Positions:

• chr11-11156267-A-G
• chr11-11156267-A-T

Variant summary

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

The ENST00000525758.1(LINC02752):​n.109-11556A>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 0.849 in 152,030 control chromosomes in the GnomAD database, including 56,033 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 0.85 (56033 hom., cov: 32)
• Consequence: LINC02752 ENST00000525758.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.42

Genes affected

LINC02752 (HGNC:54272): (long intergenic non-protein coding RNA 2752)

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.95 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC02752	XR_007062591.1	n.99-11556A>G		intron_variant, non_coding_transcript_variant
LOC105376548	XR_007062592.1	n.141+154T>C		intron_variant, non_coding_transcript_variant
LOC105376548	XR_001748126.3	n.141+154T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02752	ENST00000525758.1	n.109-11556A>G		intron_variant, non_coding_transcript_variant		1
LINC02752	ENST00000647635.1	n.273-12814A>G		intron_variant, non_coding_transcript_variant
	ENST00000702252.1	n.119+154T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.849 AC: 129049 AN: 151912 Hom.: 56012 Cov.: 32

Gnomad AFR AF: 0.651

Gnomad AMI AF: 0.943

Gnomad AMR AF: 0.860

Gnomad ASJ AF: 0.962

Gnomad EAS AF: 0.973

Gnomad SAS AF: 0.953

Gnomad FIN AF: 0.930

Gnomad MID AF: 0.934

Gnomad NFE AF: 0.930

Gnomad OTH AF: 0.880

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

GnomAD4 genome AF: 0.849 AC: 129120 AN: 152030 Hom.: 56033 Cov.: 32 AF XY: 0.852 AC XY: 63301 AN XY: 74324

Gnomad4 AFR AF: 0.651

Gnomad4 AMR AF: 0.860

Gnomad4 ASJ AF: 0.962

Gnomad4 EAS AF: 0.973

Gnomad4 SAS AF: 0.954

Gnomad4 FIN AF: 0.930

Gnomad4 NFE AF: 0.930

Gnomad4 OTH AF: 0.881

Alfa AF: 0.912 Hom.: 24260

Bravo AF: 0.837

Asia WGS AF: 0.939 AC: 3264 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	4.2
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2403456; hg19: chr11-11177814;