ENST00000443778.3:n.748-107G>A

Variant names:

• chr13-23470407-G-A
• rs2274928
• ENST00000443778.3:n.748-107G>A

Variant summary

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

The ENST00000443778.3(LINC00327):​n.748-107G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.583 in 152,092 control chromosomes in the GnomAD database, including 26,792 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 0.58 (26792 hom., cov: 33)
  • Failed GnomAD Quality Control
• Consequence: LINC00327 ENST00000443778.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.273
• Publications: 5 publications found

Genes affected

LINC00327 (HGNC:42009): (long intergenic non-protein coding RNA 327)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.736 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC00327	NR_038995.1	n.681-107G>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00327	ENST00000443778.3	n.748-107G>A		intron_variant	Intron 1 of 2	1
LINC00327	ENST00000575689.4	n.594-107G>A		intron_variant	Intron 1 of 1	1
LINC00327	ENST00000576696.2	n.1180-107G>A		intron_variant	Intron 1 of 1	1

Frequencies

GnomAD3 genomes AF: 0.582 AC: 88517 AN: 151974 Hom.: 26757 Cov.: 33

Gnomad AFR AF: 0.743

Gnomad AMI AF: 0.647

Gnomad AMR AF: 0.527

Gnomad ASJ AF: 0.548

Gnomad EAS AF: 0.471

Gnomad SAS AF: 0.367

Gnomad FIN AF: 0.556

Gnomad MID AF: 0.630

Gnomad NFE AF: 0.526

Gnomad OTH AF: 0.570

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

GnomAD4 genome AF: 0.583 AC: 88596 AN: 152092 Hom.: 26792 Cov.: 33 AF XY: 0.580 AC XY: 43111 AN XY: 74354

African (AFR) AF: 0.743 AC: 30845 AN: 41498

American (AMR) AF: 0.526 AC: 8043 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.548 AC: 1897 AN: 3464

East Asian (EAS) AF: 0.470 AC: 2436 AN: 5178

South Asian (SAS) AF: 0.368 AC: 1770 AN: 4816

European-Finnish (FIN) AF: 0.556 AC: 5870 AN: 10556

Middle Eastern (MID) AF: 0.622 AC: 183 AN: 294

European-Non Finnish (NFE) AF: 0.526 AC: 35763 AN: 67974

Other (OTH) AF: 0.568 AC: 1199 AN: 2112

Alfa AF: 0.540 Hom.: 71104

Bravo AF: 0.591

Asia WGS AF: 0.428 AC: 1492 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.1
DANN	Benign	0.69
PhyloP100		0.27

Splicing

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

Other links and lift over

dbSNP: rs2274928; hg19: chr13-24044546;