rs11022983

Variant names:

• chr11-13841677-C-T
• rs11022983
• ENST00000530492.1:n.79-14397G>A

Variant summary

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

The ENST00000530492.1(LINC02545):​n.79-14397G>A variant causes a intron 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: LINC02545 ENST00000530492.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.629
• Publications: 0 publications found

Genes affected

LINC02545 (HGNC:53580): (long intergenic non-protein coding RNA 2545)

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LINC02548	NR_149108.1	n.201-6030C>T		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02545	ENST00000530492.1	n.79-14397G>A		intron_variant	Intron 1 of 1	3
LINC02548	ENST00000531749.1	n.189-6030C>T		intron_variant	Intron 2 of 2	3
LINC02548	ENST00000648524.1	n.779+830C>T		intron_variant	Intron 4 of 6

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

African (AFR) AF: 0.231 AC: 9603 AN: 41510

American (AMR) AF: 0.115 AC: 1764 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.171 AC: 593 AN: 3470

East Asian (EAS) AF: 0.104 AC: 537 AN: 5180

South Asian (SAS) AF: 0.119 AC: 573 AN: 4820

European-Finnish (FIN) AF: 0.0250 AC: 265 AN: 10616

Middle Eastern (MID) AF: 0.153 AC: 45 AN: 294

European-Non Finnish (NFE) AF: 0.0758 AC: 5159 AN: 68020

Other (OTH) AF: 0.122 AC: 258 AN: 2110

Alfa AF: 0.0902 Hom.: 391

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
PhyloP100		0.63

Splicing

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

Other links and lift over

dbSNP: rs11022983; hg19: chr11-13863224;