13-89413849-A-G

Position:

• chr13-89413849-A-G

Variant summary

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

The ENST00000659314.1(LINC02336):​n.112-582A>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 0.177 in 152,102 control chromosomes in the GnomAD database, including 2,652 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 0.18 (2652 hom., cov: 32)
• Consequence: LINC02336 ENST00000659314.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.276

Genes affected

LINC02336 (HGNC:53256): (long intergenic non-protein coding RNA 2336)

LOC107984621 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.25 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107984621	XR_001749953.2	n.198-582A>G		intron_variant, non_coding_transcript_variant
LOC107984621	XR_001749952.2	n.64-582A>G		intron_variant, non_coding_transcript_variant
LOC107984621	XR_001749954.2	n.260-582A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02336	ENST00000659314.1	n.112-582A>G		intron_variant, non_coding_transcript_variant
LINC02336	ENST00000670662.1	n.260-582A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.176 AC: 26816 AN: 151984 Hom.: 2644 Cov.: 32

Gnomad AFR AF: 0.254

Gnomad AMI AF: 0.117

Gnomad AMR AF: 0.155

Gnomad ASJ AF: 0.269

Gnomad EAS AF: 0.0476

Gnomad SAS AF: 0.147

Gnomad FIN AF: 0.0866

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.155

Gnomad OTH AF: 0.192

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

GnomAD4 genome AF: 0.177 AC: 26855 AN: 152102 Hom.: 2652 Cov.: 32 AF XY: 0.173 AC XY: 12847 AN XY: 74374

Gnomad4 AFR AF: 0.254

Gnomad4 AMR AF: 0.155

Gnomad4 ASJ AF: 0.269

Gnomad4 EAS AF: 0.0473

Gnomad4 SAS AF: 0.147

Gnomad4 FIN AF: 0.0866

Gnomad4 NFE AF: 0.155

Gnomad4 OTH AF: 0.190

Alfa AF: 0.165 Hom.: 1155

Bravo AF: 0.184

Asia WGS AF: 0.110 AC: 385 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	1.8
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1472716; hg19: chr13-90066103;