rs17347854

Positions:

• chr11-11226295-T-C

Variant summary

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

The XR_007062591.1(LINC02752):​n.1942-1784T>C 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 0.125 in 152,106 control chromosomes in the GnomAD database, including 1,255 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 0.13 (1255 hom., cov: 32)
• Consequence: LINC02752 XR_007062591.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.839

Genes affected

LINC02752 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.147 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC02752	XR_007062591.1	n.1942-1784T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.125 AC: 19032 AN: 151988 Hom.: 1255 Cov.: 32

Gnomad AFR AF: 0.0928

Gnomad AMI AF: 0.170

Gnomad AMR AF: 0.132

Gnomad ASJ AF: 0.158

Gnomad EAS AF: 0.0535

Gnomad SAS AF: 0.133

Gnomad FIN AF: 0.0978

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.150

Gnomad OTH AF: 0.133

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

GnomAD4 genome AF: 0.125 AC: 19050 AN: 152106 Hom.: 1255 Cov.: 32 AF XY: 0.125 AC XY: 9265 AN XY: 74344

Gnomad4 AFR AF: 0.0929

Gnomad4 AMR AF: 0.132

Gnomad4 ASJ AF: 0.158

Gnomad4 EAS AF: 0.0536

Gnomad4 SAS AF: 0.132

Gnomad4 FIN AF: 0.0978

Gnomad4 NFE AF: 0.150

Gnomad4 OTH AF: 0.134

Alfa AF: 0.146 Hom.: 2166

Bravo AF: 0.123

Asia WGS AF: 0.0980 AC: 340 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.2
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17347854; hg19: chr11-11247842;