5-6767199-T-G

Variant names:

• chr5-6767199-T-G
• rs12520016
• ENST00000506093.1:n.92-1076T>G

Variant summary

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

The ENST00000506093.1(LINC02236):​n.92-1076T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0673 in 151,780 control chromosomes in the GnomAD database, including 418 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 0.067 (418 hom., cov: 33)
• Consequence: LINC02236 ENST00000506093.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.227
• Publications: 9 publications found

Genes affected

LINC02236 (HGNC:53107): (long intergenic non-protein coding RNA 2236)

LOC102724943 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.113 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC102724943	XR_007059141.1	n.52+836T>G		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02236	ENST00000506093.1	n.92-1076T>G		intron_variant	Intron 1 of 2	4
LINC02236	ENST00000649262.1	n.88+1218T>G		intron_variant	Intron 1 of 1
LINC02236	ENST00000688820.2	n.47+1218T>G		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.0674 AC: 10216 AN: 151682 Hom.: 418 Cov.: 33

Gnomad AFR AF: 0.116

Gnomad AMI AF: 0.119

Gnomad AMR AF: 0.0439

Gnomad ASJ AF: 0.0407

Gnomad EAS AF: 0.000580

Gnomad SAS AF: 0.0193

Gnomad FIN AF: 0.0828

Gnomad MID AF: 0.0637

Gnomad NFE AF: 0.0501

Gnomad OTH AF: 0.0639

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

GnomAD4 genome AF: 0.0673 AC: 10222 AN: 151780 Hom.: 418 Cov.: 33 AF XY: 0.0668 AC XY: 4956 AN XY: 74164

African (AFR) AF: 0.116 AC: 4785 AN: 41374

American (AMR) AF: 0.0438 AC: 669 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.0407 AC: 141 AN: 3468

East Asian (EAS) AF: 0.000581 AC: 3 AN: 5160

South Asian (SAS) AF: 0.0189 AC: 91 AN: 4814

European-Finnish (FIN) AF: 0.0828 AC: 867 AN: 10466

Middle Eastern (MID) AF: 0.0651 AC: 19 AN: 292

European-Non Finnish (NFE) AF: 0.0501 AC: 3406 AN: 67928

Other (OTH) AF: 0.0632 AC: 133 AN: 2104

Alfa AF: 0.0522 Hom.: 535

Bravo AF: 0.0672

Asia WGS AF: 0.0140 AC: 51 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.1
DANN	Benign	0.39
PhyloP100		-0.23

Splicing

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

Other links and lift over

dbSNP: rs12520016; hg19: chr5-6767312;