rs434949

Variant names:

• chr11-29580727-A-G
• rs434949
• ENST00000525097.1:n.70+13499T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000525097.1(LINC02755):​n.70+13499T>C variant causes a intron 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 ENST00000525097.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.178
• Publications: 4 publications found

Genes affected

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

LINC02546 (HGNC:53581): (long intergenic non-protein coding RNA 2546)

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LINC02755	NR_183753.1	n.125+13499T>C		intron_variant	Intron 1 of 5
LINC02755	NR_183754.1	n.125+13499T>C		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02755	ENST00000525097.1	n.70+13499T>C		intron_variant	Intron 1 of 3	3
LINC02755	ENST00000528553.2	n.207+33368T>C		intron_variant	Intron 3 of 6	3
LINC02755	ENST00000653616.1	n.125+13499T>C		intron_variant	Intron 1 of 5

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

African (AFR) AF: 0.854 AC: 35408 AN: 41448

American (AMR) AF: 0.351 AC: 5337 AN: 15212

Ashkenazi Jewish (ASJ) AF: 0.431 AC: 1493 AN: 3466

East Asian (EAS) AF: 0.257 AC: 1320 AN: 5132

South Asian (SAS) AF: 0.395 AC: 1901 AN: 4818

European-Finnish (FIN) AF: 0.354 AC: 3733 AN: 10532

Middle Eastern (MID) AF: 0.408 AC: 120 AN: 294

European-Non Finnish (NFE) AF: 0.408 AC: 27717 AN: 67862

Other (OTH) AF: 0.500 AC: 1052 AN: 2106

Alfa AF: 0.472 Hom.: 2963

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
PhyloP100		-0.18

Splicing

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

Other links and lift over

dbSNP: rs434949; hg19: chr11-29602274;