13-42867197-C-T

Variant names:

• chr13-42867197-C-T
• rs1535891
• ENST00000828781.1:n.183-5032G>A

Variant summary

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

The ENST00000828781.1(LINC00428):​n.183-5032G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.724 in 151,992 control chromosomes in the GnomAD database, including 39,976 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 0.72 (39976 hom., cov: 31)
• Consequence: LINC00428 ENST00000828781.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.29
• Publications: 5 publications found

Genes affected

LINC00428 (HGNC:42763): (long intergenic non-protein coding RNA 428)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.83 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC00428	NR_126388.1	n.188-5032G>A		intron_variant	Intron 1 of 2
LINC00428	NR_126389.1	n.289+3404G>A		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00428	ENST00000828781.1	n.183-5032G>A		intron_variant	Intron 1 of 3
LINC00428	ENST00000828782.1	n.247-5032G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.724 AC: 110010 AN: 151874 Hom.: 39947 Cov.: 31

Gnomad AFR AF: 0.740

Gnomad AMI AF: 0.709

Gnomad AMR AF: 0.738

Gnomad ASJ AF: 0.732

Gnomad EAS AF: 0.851

Gnomad SAS AF: 0.768

Gnomad FIN AF: 0.718

Gnomad MID AF: 0.766

Gnomad NFE AF: 0.700

Gnomad OTH AF: 0.723

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

GnomAD4 genome AF: 0.724 AC: 110092 AN: 151992 Hom.: 39976 Cov.: 31 AF XY: 0.727 AC XY: 53967 AN XY: 74260

African (AFR) AF: 0.740 AC: 30666 AN: 41452

American (AMR) AF: 0.738 AC: 11268 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.732 AC: 2538 AN: 3468

East Asian (EAS) AF: 0.851 AC: 4391 AN: 5160

South Asian (SAS) AF: 0.768 AC: 3694 AN: 4808

European-Finnish (FIN) AF: 0.718 AC: 7582 AN: 10558

Middle Eastern (MID) AF: 0.769 AC: 226 AN: 294

European-Non Finnish (NFE) AF: 0.700 AC: 47547 AN: 67962

Other (OTH) AF: 0.727 AC: 1533 AN: 2110

Alfa AF: 0.701 Hom.: 8006

Bravo AF: 0.725

Asia WGS AF: 0.812 AC: 2821 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.11
DANN	Benign	0.57
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs1535891; hg19: chr13-43441333;