11-41661360-G-T

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 8 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000526978.5. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02741	ENST00000526978.5	TSL:3	n.150-40961C>A		intron	N/A
	LINC02741	ENST00000531210.1	TSL:3	n.60+50989C>A		intron	N/A
	LINC02741	ENST00000655470.1		n.153+50989C>A		intron	N/A

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

African (AFR) AF: 0.515 AC: 21326 AN: 41424

American (AMR) AF: 0.836 AC: 12792 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.924 AC: 3206 AN: 3468

East Asian (EAS) AF: 0.903 AC: 4671 AN: 5170

South Asian (SAS) AF: 0.838 AC: 4045 AN: 4828

European-Finnish (FIN) AF: 0.871 AC: 9245 AN: 10610

Middle Eastern (MID) AF: 0.867 AC: 255 AN: 294

European-Non Finnish (NFE) AF: 0.873 AC: 59340 AN: 68004

Other (OTH) AF: 0.824 AC: 1741 AN: 2114

Alfa AF: 0.841 Hom.: 23680

Bravo AF: 0.758

Asia WGS AF: 0.870 AC: 3026 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.2
DANN	Benign	0.42
PhyloP100		-0.15

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs899036;

hg19: chr11-41682910;