5-6791794-A-G

Position:

• chr5-6791794-A-G

Variant summary

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

The ENST00000691419.1(LINC02236):​n.714+14285A>G 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 0.531 in 152,056 control chromosomes in the GnomAD database, including 21,536 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 0.53 (21536 hom., cov: 32)
• Consequence: LINC02236 ENST00000691419.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.771

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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.613 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02236	ENST00000691419.1	n.714+14285A>G		intron_variant, non_coding_transcript_variant
LINC02236	ENST00000648399.1	n.497+14285A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.531 AC: 80646 AN: 151938 Hom.: 21535 Cov.: 32

Gnomad AFR AF: 0.531

Gnomad AMI AF: 0.554

Gnomad AMR AF: 0.508

Gnomad ASJ AF: 0.557

Gnomad EAS AF: 0.631

Gnomad SAS AF: 0.481

Gnomad FIN AF: 0.521

Gnomad MID AF: 0.509

Gnomad NFE AF: 0.532

Gnomad OTH AF: 0.510

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

GnomAD4 genome AF: 0.531 AC: 80678 AN: 152056 Hom.: 21536 Cov.: 32 AF XY: 0.530 AC XY: 39425 AN XY: 74358

Gnomad4 AFR AF: 0.530

Gnomad4 AMR AF: 0.508

Gnomad4 ASJ AF: 0.557

Gnomad4 EAS AF: 0.631

Gnomad4 SAS AF: 0.482

Gnomad4 FIN AF: 0.521

Gnomad4 NFE AF: 0.533

Gnomad4 OTH AF: 0.506

Alfa AF: 0.382 Hom.: 955

Bravo AF: 0.530

Asia WGS AF: 0.571 AC: 1986 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.1
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs400328; hg19: chr5-6791907;