11-91222804-C-T

Variant names:

• chr11-91222804-C-T
• rs4483549
• ENST00000526509.2:n.746-11332C>T

Variant summary

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

The ENST00000526509.2(LINC02748):​n.746-11332C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.356 in 151,560 control chromosomes in the GnomAD database, including 9,839 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 0.36 (9839 hom., cov: 31)
• Consequence: LINC02748 ENST00000526509.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.719
• Publications: 5 publications found

Genes affected

LINC02748 (HGNC:54267): (long intergenic non-protein coding RNA 2748)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.517 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000526509.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02748	NR_183632.1		n.779-5178C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02748	ENST00000526509.2	TSL:3	n.746-11332C>T		intron	N/A
	LINC02748	ENST00000724586.1		n.756-5178C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.357 AC: 54007 AN: 151442 Hom.: 9831 Cov.: 31

Gnomad AFR AF: 0.308

Gnomad AMI AF: 0.329

Gnomad AMR AF: 0.344

Gnomad ASJ AF: 0.282

Gnomad EAS AF: 0.533

Gnomad SAS AF: 0.305

Gnomad FIN AF: 0.414

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.376

Gnomad OTH AF: 0.339

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

GnomAD4 genome AF: 0.356 AC: 54024 AN: 151560 Hom.: 9839 Cov.: 31 AF XY: 0.359 AC XY: 26599 AN XY: 74030

African (AFR) AF: 0.307 AC: 12706 AN: 41384

American (AMR) AF: 0.343 AC: 5202 AN: 15162

Ashkenazi Jewish (ASJ) AF: 0.282 AC: 976 AN: 3460

East Asian (EAS) AF: 0.534 AC: 2701 AN: 5060

South Asian (SAS) AF: 0.306 AC: 1472 AN: 4808

European-Finnish (FIN) AF: 0.414 AC: 4358 AN: 10528

Middle Eastern (MID) AF: 0.349 AC: 102 AN: 292

European-Non Finnish (NFE) AF: 0.376 AC: 25481 AN: 67848

Other (OTH) AF: 0.345 AC: 727 AN: 2110

Alfa AF: 0.364 Hom.: 45804

Bravo AF: 0.351

Asia WGS AF: 0.394 AC: 1369 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.57
DANN	Benign	0.44
PhyloP100		-0.72

Splicing

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

Other links and lift over

dbSNP: rs4483549; hg19: chr11-90955972;