rs275456

chr5-6813824-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_146281.1(LINC02236):n.467-12819G>T variant causes a intron, non coding transcript 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 NR_146281.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.40

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02236	NR_146281.1	n.467-12819G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02236	ENST00000691419.1	n.715-12819G>T		intron_variant, non_coding_transcript_variant
LINC02236	ENST00000508881.1	n.467-12819G>T		intron_variant, non_coding_transcript_variant		4
LINC02236	ENST00000648399.1	n.498-12819G>T		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.0605

Gnomad4 AMR AF: 0.265

Gnomad4 ASJ AF: 0.242

Gnomad4 EAS AF: 0.214

Gnomad4 SAS AF: 0.320

Gnomad4 FIN AF: 0.241

Gnomad4 NFE AF: 0.252

Gnomad4 OTH AF: 0.229

Alfa AF: 0.248 Hom.: 6046

Bravo AF: 0.194

Asia WGS AF: 0.245 AC: 854 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.45
Dann	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs275456; hg19: chr5-6813937;