5-6788169-A-G

Position:

• chr5-6788169-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+10660A>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 0.744 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 ENST00000691419.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.172

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=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.839 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02236	ENST00000691419.1	n.714+10660A>G		intron_variant, non_coding_transcript_variant
LINC02236	ENST00000648399.1	n.497+10660A>G		intron_variant, non_coding_transcript_variant
LINC02236	ENST00000690700.1	n.810-3299A>G		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.675

Gnomad4 AMR AF: 0.804

Gnomad4 ASJ AF: 0.768

Gnomad4 EAS AF: 0.860

Gnomad4 SAS AF: 0.843

Gnomad4 FIN AF: 0.701

Gnomad4 NFE AF: 0.762

Gnomad4 OTH AF: 0.742

Alfa AF: 0.721 Hom.: 6301

Bravo AF: 0.749

Asia WGS AF: 0.841 AC: 2925 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs274646; hg19: chr5-6788282;