13-63997994-C-T

Variant names:

• chr13-63997994-C-T
• rs9539891
• ENST00000456627.1:n.1104+4391G>A

Variant summary

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

The ENST00000456627.1(LINC00355):​n.1104+4391G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.533 in 151,836 control chromosomes in the GnomAD database, including 24,437 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 0.53 (24437 hom., cov: 31)
• Consequence: LINC00355 ENST00000456627.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.07

Genes affected

LINC00355 (HGNC:27061): (long intergenic non-protein coding RNA 355)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.66 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC00355	NR_145420.1	n.1104+4391G>A		intron_variant	Intron 4 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00355	ENST00000456627.1	n.1104+4391G>A		intron_variant	Intron 4 of 5	2
LINC00355	ENST00000650541.1	n.1137+4391G>A		intron_variant	Intron 4 of 6
LINC00355	ENST00000654282.1	n.802+4391G>A		intron_variant	Intron 2 of 2
LINC00355	ENST00000669788.1	n.1119+4391G>A		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.533 AC: 80922 AN: 151718 Hom.: 24431 Cov.: 31

Gnomad AFR AF: 0.235

Gnomad AMI AF: 0.616

Gnomad AMR AF: 0.568

Gnomad ASJ AF: 0.612

Gnomad EAS AF: 0.666

Gnomad SAS AF: 0.515

Gnomad FIN AF: 0.707

Gnomad MID AF: 0.617

Gnomad NFE AF: 0.665

Gnomad OTH AF: 0.555

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

GnomAD4 genome AF: 0.533 AC: 80955 AN: 151836 Hom.: 24437 Cov.: 31 AF XY: 0.535 AC XY: 39715 AN XY: 74224

Gnomad4 AFR AF: 0.235

Gnomad4 AMR AF: 0.568

Gnomad4 ASJ AF: 0.612

Gnomad4 EAS AF: 0.666

Gnomad4 SAS AF: 0.515

Gnomad4 FIN AF: 0.707

Gnomad4 NFE AF: 0.665

Gnomad4 OTH AF: 0.559

Alfa AF: 0.624 Hom.: 13930

Bravo AF: 0.512

Asia WGS AF: 0.582 AC: 2022 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.4
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9539891; hg19: chr13-64572127;