chr13-73550101-C-T

Position:

• chr13-73550101-C-T

Variant summary

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

The NR_184171.1(LINC00393):​n.143-3260G>A 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 0.0894 in 151,950 control chromosomes in the GnomAD database, including 1,597 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 0.089 (1597 hom., cov: 32)
• Consequence: LINC00393 NR_184171.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.99

Genes affected

LINC00393 (HGNC:42721): (long intergenic non-protein coding RNA 393)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.582 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC00393	NR_184171.1	n.143-3260G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00393	ENST00000452852.2	n.32-3260G>A		intron_variant, non_coding_transcript_variant		3
LINC00393	ENST00000647940.1	n.129-3260G>A		intron_variant, non_coding_transcript_variant
LINC00393	ENST00000648624.1	n.131-3260G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0893 AC: 13554 AN: 151834 Hom.: 1597 Cov.: 32

Gnomad AFR AF: 0.154

Gnomad AMI AF: 0.143

Gnomad AMR AF: 0.0427

Gnomad ASJ AF: 0.0527

Gnomad EAS AF: 0.599

Gnomad SAS AF: 0.164

Gnomad FIN AF: 0.0891

Gnomad MID AF: 0.0478

Gnomad NFE AF: 0.0185

Gnomad OTH AF: 0.0712

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

GnomAD4 genome AF: 0.0894 AC: 13577 AN: 151950 Hom.: 1597 Cov.: 32 AF XY: 0.0964 AC XY: 7160 AN XY: 74256

Gnomad4 AFR AF: 0.154

Gnomad4 AMR AF: 0.0427

Gnomad4 ASJ AF: 0.0527

Gnomad4 EAS AF: 0.599

Gnomad4 SAS AF: 0.165

Gnomad4 FIN AF: 0.0891

Gnomad4 NFE AF: 0.0185

Gnomad4 OTH AF: 0.0719

Alfa AF: 0.0534 Hom.: 77

Bravo AF: 0.0916

Asia WGS AF: 0.316 AC: 1098 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.10
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9318189; hg19: chr13-74124238;