rs75900745

Variant names:

• chr4-137169858-A-G
• rs75900745
• ENST00000505736.5:n.63+42879T>C

Variant summary

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

The ENST00000505736.5(LINC02511):​n.63+42879T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0794 in 152,188 control chromosomes in the GnomAD database, including 566 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 0.079 (566 hom., cov: 31)
• Consequence: LINC02511 ENST00000505736.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.40
• Publications: 2 publications found

Genes affected

LINC02511 (HGNC:53500): (long intergenic non-protein coding RNA 2511)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.15 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000505736.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02511	NR_149105.1		n.63+42879T>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02511	ENST00000505736.5	TSL:5	n.63+42879T>C		intron	N/A
	LINC02511	ENST00000652184.1		n.54+42879T>C		intron	N/A
	LINC02511	ENST00000656187.1		n.52+42879T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0794 AC: 12082 AN: 152072 Hom.: 566 Cov.: 31

Gnomad AFR AF: 0.0506

Gnomad AMI AF: 0.104

Gnomad AMR AF: 0.0779

Gnomad ASJ AF: 0.127

Gnomad EAS AF: 0.107

Gnomad SAS AF: 0.160

Gnomad FIN AF: 0.109

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.0821

Gnomad OTH AF: 0.0781

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

GnomAD4 genome AF: 0.0794 AC: 12083 AN: 152188 Hom.: 566 Cov.: 31 AF XY: 0.0830 AC XY: 6177 AN XY: 74414

African (AFR) AF: 0.0505 AC: 2099 AN: 41534

American (AMR) AF: 0.0777 AC: 1187 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.127 AC: 440 AN: 3472

East Asian (EAS) AF: 0.107 AC: 552 AN: 5182

South Asian (SAS) AF: 0.159 AC: 768 AN: 4818

European-Finnish (FIN) AF: 0.109 AC: 1160 AN: 10600

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.0821 AC: 5580 AN: 67994

Other (OTH) AF: 0.0811 AC: 171 AN: 2108

Alfa AF: 0.0836 Hom.: 159

Bravo AF: 0.0769

Asia WGS AF: 0.148 AC: 515 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	8.4
DANN	Benign	0.49
PhyloP100		1.4

Splicing

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

Other links and lift over

dbSNP: rs75900745; hg19: chr4-138091012;