rs11022983

chr11-13841677-C-T

Variant summary

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

The NR_149108.1(LINC02548):n.201-6030C>T 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 0.124 in 152,218 control chromosomes in the GnomAD database, including 1,585 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 0.12 (1585 hom., cov: 33)
• Consequence: LINC02548 NR_149108.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.629

Genes affected

(HGNC:):

LINC02548 (HGNC:53583): (long intergenic non-protein coding RNA 2548)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.227 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02548	NR_149108.1	n.201-6030C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000530492.1	n.79-14397G>A		intron_variant, non_coding_transcript_variant		3
LINC02548	ENST00000664710.1	n.766+826C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.124 AC: 18888 AN: 152100 Hom.: 1582 Cov.: 33

Gnomad AFR AF: 0.231

Gnomad AMI AF: 0.126

Gnomad AMR AF: 0.116

Gnomad ASJ AF: 0.171

Gnomad EAS AF: 0.104

Gnomad SAS AF: 0.119

Gnomad FIN AF: 0.0250

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.0758

Gnomad OTH AF: 0.123

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

GnomAD4 genome AF: 0.124 AC: 18912 AN: 152218 Hom.: 1585 Cov.: 33 AF XY: 0.121 AC XY: 8979 AN XY: 74426

Gnomad4 AFR AF: 0.231

Gnomad4 AMR AF: 0.115

Gnomad4 ASJ AF: 0.171

Gnomad4 EAS AF: 0.104

Gnomad4 SAS AF: 0.119

Gnomad4 FIN AF: 0.0250

Gnomad4 NFE AF: 0.0758

Gnomad4 OTH AF: 0.122

Alfa AF: 0.0886 Hom.: 330

Bravo AF: 0.137

Asia WGS AF: 0.127 AC: 442 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	6.4
Dann	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11022983; hg19: chr11-13863224;