4-137200730-A-G

Variant names:

• chr4-137200730-A-G
• rs6854244
• ENST00000505736.5:n.63+12007T>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+12007T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.494 in 152,022 control chromosomes in the GnomAD database, including 20,165 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 0.49 (20165 hom., cov: 32)
• Consequence: LINC02511 ENST00000505736.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.160
• Publications: 8 publications found

Genes affected

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

LINC02510 (HGNC:53499): (long intergenic non-protein coding RNA 2510)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.612 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02511	NR_149105.1	n.63+12007T>C		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02511	ENST00000505736.5	n.63+12007T>C		intron_variant	Intron 1 of 3	5
LINC02511	ENST00000652184.1	n.54+12007T>C		intron_variant	Intron 1 of 5
LINC02511	ENST00000656187.1	n.52+12007T>C		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.494 AC: 75099 AN: 151904 Hom.: 20166 Cov.: 32

Gnomad AFR AF: 0.276

Gnomad AMI AF: 0.784

Gnomad AMR AF: 0.489

Gnomad ASJ AF: 0.546

Gnomad EAS AF: 0.631

Gnomad SAS AF: 0.547

Gnomad FIN AF: 0.586

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.594

Gnomad OTH AF: 0.503

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

GnomAD4 genome AF: 0.494 AC: 75117 AN: 152022 Hom.: 20165 Cov.: 32 AF XY: 0.496 AC XY: 36834 AN XY: 74276

African (AFR) AF: 0.276 AC: 11437 AN: 41474

American (AMR) AF: 0.489 AC: 7459 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.546 AC: 1895 AN: 3468

East Asian (EAS) AF: 0.630 AC: 3259 AN: 5170

South Asian (SAS) AF: 0.545 AC: 2623 AN: 4810

European-Finnish (FIN) AF: 0.586 AC: 6179 AN: 10546

Middle Eastern (MID) AF: 0.432 AC: 127 AN: 294

European-Non Finnish (NFE) AF: 0.594 AC: 40356 AN: 67976

Other (OTH) AF: 0.506 AC: 1067 AN: 2108

Alfa AF: 0.567 Hom.: 16505

Bravo AF: 0.481

Asia WGS AF: 0.593 AC: 2063 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.0
DANN	Benign	0.75
PhyloP100		-0.16

Splicing

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

Other links and lift over

dbSNP: rs6854244; hg19: chr4-138121884;