rs7480010

chr11-42225168-G-Achr11-42225168-G-Cchr11-42225168-G-T

Variant summary

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

The NR_038309.1(LINC02740):n.332+12925C>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 0.562 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 NR_038309.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.614

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02740	NR_038309.1	n.332+12925C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02740	ENST00000658612.1	n.509+12925C>T		intron_variant, non_coding_transcript_variant
LINC02740	ENST00000525641.5	n.177+12925C>T		intron_variant, non_coding_transcript_variant		3
LINC02740	ENST00000527757.2	n.355-10182C>T		intron_variant, non_coding_transcript_variant		3
LINC02740	ENST00000530387.5	n.93+12925C>T		intron_variant, non_coding_transcript_variant		5

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

Gnomad4 AFR AF: 0.135

Gnomad4 AMR AF: 0.713

Gnomad4 ASJ AF: 0.595

Gnomad4 EAS AF: 0.803

Gnomad4 SAS AF: 0.607

Gnomad4 FIN AF: 0.832

Gnomad4 NFE AF: 0.723

Gnomad4 OTH AF: 0.586

Alfa AF: 0.688 Hom.: 76918

Bravo AF: 0.535

Asia WGS AF: 0.627 AC: 2180 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	0.14
Dann	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7480010; hg19: chr11-42246718;