rs434949

Positions:

• chr11-29580727-A-G

Variant summary

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

The NR_183754.1(LINC02755):​n.125+13499T>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 0.517 in 151,782 control chromosomes in the GnomAD database, including 23,788 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 0.52 (23788 hom., cov: 32)
• Consequence: LINC02755 NR_183754.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.178

Genes affected

LINC02755 (HGNC:54275): (long intergenic non-protein coding RNA 2755)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.847 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02755	NR_183754.1	n.125+13499T>C		intron_variant, non_coding_transcript_variant
LINC02755	NR_183753.1	n.125+13499T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02755	ENST00000657392.1	n.231+33368T>C		intron_variant, non_coding_transcript_variant
LINC02755	ENST00000525097.1	n.70+13499T>C		intron_variant, non_coding_transcript_variant		3
LINC02755	ENST00000528553.2	n.207+33368T>C		intron_variant, non_coding_transcript_variant		3
LINC02755	ENST00000653616.1	n.125+13499T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.517 AC: 78400 AN: 151664 Hom.: 23744 Cov.: 32

Gnomad AFR AF: 0.854

Gnomad AMI AF: 0.455

Gnomad AMR AF: 0.351

Gnomad ASJ AF: 0.431

Gnomad EAS AF: 0.257

Gnomad SAS AF: 0.396

Gnomad FIN AF: 0.354

Gnomad MID AF: 0.414

Gnomad NFE AF: 0.409

Gnomad OTH AF: 0.496

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

GnomAD4 genome AF: 0.517 AC: 78496 AN: 151782 Hom.: 23788 Cov.: 32 AF XY: 0.507 AC XY: 37626 AN XY: 74168

Gnomad4 AFR AF: 0.854

Gnomad4 AMR AF: 0.351

Gnomad4 ASJ AF: 0.431

Gnomad4 EAS AF: 0.257

Gnomad4 SAS AF: 0.395

Gnomad4 FIN AF: 0.354

Gnomad4 NFE AF: 0.408

Gnomad4 OTH AF: 0.500

Alfa AF: 0.459 Hom.: 2686

Bravo AF: 0.530

Asia WGS AF: 0.376 AC: 1303 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.3
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs434949; hg19: chr11-29602274;