5-6813824-G-T

Variant names:

• chr5-6813824-G-T
• rs275456
• ENST00000508881.1:n.467-12819G>T

Variant summary

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

The ENST00000508881.1(LINC02236):​n.467-12819G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.2 in 152,212 control chromosomes in the GnomAD database, including 3,786 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 0.20 (3786 hom., cov: 33)
• Consequence: LINC02236 ENST00000508881.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.40
• Publications: 6 publications found

Genes affected

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.307 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000508881.1. 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
	LINC02236	NR_146281.1		n.467-12819G>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02236	ENST00000508881.1	TSL:4	n.467-12819G>T		intron	N/A
	LINC02236	ENST00000648399.1		n.498-12819G>T		intron	N/A
	LINC02236	ENST00000691419.2		n.715-12819G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.200 AC: 30479 AN: 152094 Hom.: 3780 Cov.: 33

Gnomad AFR AF: 0.0605

Gnomad AMI AF: 0.209

Gnomad AMR AF: 0.265

Gnomad ASJ AF: 0.242

Gnomad EAS AF: 0.214

Gnomad SAS AF: 0.320

Gnomad FIN AF: 0.241

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.252

Gnomad OTH AF: 0.226

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

GnomAD4 genome AF: 0.200 AC: 30495 AN: 152212 Hom.: 3786 Cov.: 33 AF XY: 0.202 AC XY: 15022 AN XY: 74410

African (AFR) AF: 0.0605 AC: 2515 AN: 41554

American (AMR) AF: 0.265 AC: 4048 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.242 AC: 839 AN: 3466

East Asian (EAS) AF: 0.214 AC: 1106 AN: 5172

South Asian (SAS) AF: 0.320 AC: 1544 AN: 4824

European-Finnish (FIN) AF: 0.241 AC: 2552 AN: 10598

Middle Eastern (MID) AF: 0.218 AC: 64 AN: 294

European-Non Finnish (NFE) AF: 0.252 AC: 17154 AN: 67994

Other (OTH) AF: 0.229 AC: 483 AN: 2110

Alfa AF: 0.245 Hom.: 7101

Bravo AF: 0.194

Asia WGS AF: 0.245 AC: 854 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.45
DANN	Benign	0.43
PhyloP100		-2.4

Splicing

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

Other links and lift over

dbSNP: rs275456; hg19: chr5-6813937;