chr11-42225168-G-A

Variant names:

• chr11-42225168-G-A
• rs7480010
• ENST00000525641.5:n.177+12925C>T

Variant summary

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

The ENST00000525641.5(LINC02740):​n.177+12925C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.562 in 152,054 control chromosomes in the GnomAD database, including 29,537 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 0.56 (29537 hom., cov: 33)
• Consequence: LINC02740 ENST00000525641.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.614
• Publications: 31 publications found

Genes affected

LINC02740 (HGNC:54257): (long intergenic non-protein coding RNA 2740)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.783 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000525641.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02740	NR_038309.1		n.332+12925C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02740	ENST00000525641.5	TSL:3	n.177+12925C>T		intron	N/A
	LINC02740	ENST00000527757.2	TSL:3	n.355-10182C>T		intron	N/A
	LINC02740	ENST00000530387.5	TSL:5	n.93+12925C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.562 AC: 85443 AN: 151938 Hom.: 29539 Cov.: 33

Gnomad AFR AF: 0.135

Gnomad AMI AF: 0.530

Gnomad AMR AF: 0.713

Gnomad ASJ AF: 0.595

Gnomad EAS AF: 0.803

Gnomad SAS AF: 0.606

Gnomad FIN AF: 0.832

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.723

Gnomad OTH AF: 0.585

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

GnomAD4 genome AF: 0.562 AC: 85444 AN: 152054 Hom.: 29537 Cov.: 33 AF XY: 0.571 AC XY: 42417 AN XY: 74314

African (AFR) AF: 0.135 AC: 5590 AN: 41482

American (AMR) AF: 0.713 AC: 10888 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.595 AC: 2066 AN: 3470

East Asian (EAS) AF: 0.803 AC: 4147 AN: 5164

South Asian (SAS) AF: 0.607 AC: 2923 AN: 4814

European-Finnish (FIN) AF: 0.832 AC: 8807 AN: 10584

Middle Eastern (MID) AF: 0.514 AC: 151 AN: 294

European-Non Finnish (NFE) AF: 0.723 AC: 49150 AN: 67958

Other (OTH) AF: 0.586 AC: 1240 AN: 2116

Alfa AF: 0.661 Hom.: 107772

Bravo AF: 0.535

Asia WGS AF: 0.627 AC: 2180 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.14
DANN	Benign	0.70
PhyloP100		-0.61

Splicing

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

Other links and lift over

dbSNP: rs7480010; hg19: chr11-42246718;