11-41661360-G-T

Variant names:

• chr11-41661360-G-T
• rs899036
• ENST00000526978.5:n.150-40961C>A

Variant summary

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

The ENST00000526978.5(LINC02741):​n.150-40961C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.772 in 152,118 control chromosomes in the GnomAD database, including 47,332 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 0.77 (47332 hom., cov: 32)
• Consequence: LINC02741 ENST00000526978.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.152

Genes affected

LINC02741 (HGNC:54258): (long intergenic non-protein coding RNA 2741)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.882 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02741	XR_001748196.2	n.237+50989C>A		intron_variant	Intron 2 of 3
LINC02741	XR_931218.3	n.234-40961C>A		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02741	ENST00000526978.5	n.150-40961C>A		intron_variant	Intron 2 of 6	3
LINC02741	ENST00000531210.1	n.60+50989C>A		intron_variant	Intron 1 of 2	3
LINC02741	ENST00000655470.1	n.153+50989C>A		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.772 AC: 117412 AN: 152000 Hom.: 47318 Cov.: 32

Gnomad AFR AF: 0.515

Gnomad AMI AF: 0.922

Gnomad AMR AF: 0.836

Gnomad ASJ AF: 0.924

Gnomad EAS AF: 0.904

Gnomad SAS AF: 0.837

Gnomad FIN AF: 0.871

Gnomad MID AF: 0.867

Gnomad NFE AF: 0.873

Gnomad OTH AF: 0.821

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

GnomAD4 genome AF: 0.772 AC: 117460 AN: 152118 Hom.: 47332 Cov.: 32 AF XY: 0.776 AC XY: 57692 AN XY: 74390

Gnomad4 AFR AF: 0.515

Gnomad4 AMR AF: 0.836

Gnomad4 ASJ AF: 0.924

Gnomad4 EAS AF: 0.903

Gnomad4 SAS AF: 0.838

Gnomad4 FIN AF: 0.871

Gnomad4 NFE AF: 0.873

Gnomad4 OTH AF: 0.824

Alfa AF: 0.842 Hom.: 20706

Bravo AF: 0.758

Asia WGS AF: 0.870 AC: 3026 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.2
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs899036; hg19: chr11-41682910;