5-6788169-A-G

Variant names:

• chr5-6788169-A-G
• rs274646
• ENST00000648399.1:n.497+10660A>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+10660A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.744 in 152,048 control chromosomes in the GnomAD database, including 42,277 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 0.74 (42277 hom., cov: 32)
• Consequence: LINC02236 ENST00000648399.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.172
• Publications: 5 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=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.839 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000648399.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02236	ENST00000648399.1		n.497+10660A>G		intron	N/A
	LINC02236	ENST00000690700.1		n.810-3299A>G		intron	N/A
	LINC02236	ENST00000691419.2		n.714+10660A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.743 AC: 112958 AN: 151930 Hom.: 42238 Cov.: 32

Gnomad AFR AF: 0.675

Gnomad AMI AF: 0.671

Gnomad AMR AF: 0.804

Gnomad ASJ AF: 0.768

Gnomad EAS AF: 0.860

Gnomad SAS AF: 0.843

Gnomad FIN AF: 0.701

Gnomad MID AF: 0.766

Gnomad NFE AF: 0.762

Gnomad OTH AF: 0.742

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

GnomAD4 genome AF: 0.744 AC: 113053 AN: 152048 Hom.: 42277 Cov.: 32 AF XY: 0.744 AC XY: 55271 AN XY: 74320

African (AFR) AF: 0.675 AC: 27989 AN: 41448

American (AMR) AF: 0.804 AC: 12291 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.768 AC: 2665 AN: 3470

East Asian (EAS) AF: 0.860 AC: 4439 AN: 5160

South Asian (SAS) AF: 0.843 AC: 4062 AN: 4816

European-Finnish (FIN) AF: 0.701 AC: 7409 AN: 10572

Middle Eastern (MID) AF: 0.786 AC: 231 AN: 294

European-Non Finnish (NFE) AF: 0.762 AC: 51792 AN: 67992

Other (OTH) AF: 0.742 AC: 1563 AN: 2106

Alfa AF: 0.745 Hom.: 13724

Bravo AF: 0.749

Asia WGS AF: 0.841 AC: 2925 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.3
DANN	Benign	0.13
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs274646; hg19: chr5-6788282;