chr5-6791794-A-G

Variant names:

• chr5-6791794-A-G
• rs400328
• ENST00000648399.1:n.497+14285A>G

Variant summary

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

The ENST00000648399.1(LINC02236):​n.497+14285A>G variant causes a intron 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 ENST00000648399.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.771
• Publications: 4 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=-0.89).
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02236	ENST00000648399.1	n.497+14285A>G		intron_variant	Intron 3 of 6
LINC02236	ENST00000691419.2	n.714+14285A>G		intron_variant	Intron 3 of 3
LINC02236	ENST00000725827.1	n.192+14285A>G		intron_variant	Intron 1 of 1

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

African (AFR) AF: 0.530 AC: 21981 AN: 41452

American (AMR) AF: 0.508 AC: 7762 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.557 AC: 1930 AN: 3468

East Asian (EAS) AF: 0.631 AC: 3261 AN: 5166

South Asian (SAS) AF: 0.482 AC: 2315 AN: 4806

European-Finnish (FIN) AF: 0.521 AC: 5503 AN: 10566

Middle Eastern (MID) AF: 0.497 AC: 146 AN: 294

European-Non Finnish (NFE) AF: 0.533 AC: 36209 AN: 67994

Other (OTH) AF: 0.506 AC: 1067 AN: 2110

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
PhyloP100		0.77

Splicing

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

Other links and lift over

dbSNP: rs400328; hg19: chr5-6791907;