rs1535891

chr13-42867197-C-T

Variant summary

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

The NR_126389.1(LINC00428):n.289+3404G>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 0.724 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 NR_126389.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.29

Genes affected

LINC00428 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LINC00428	NR_126389.1	n.289+3404G>A		intron_variant, non_coding_transcript_variant
LINC00428	NR_126388.1	n.188-5032G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.740

Gnomad4 AMR AF: 0.738

Gnomad4 ASJ AF: 0.732

Gnomad4 EAS AF: 0.851

Gnomad4 SAS AF: 0.768

Gnomad4 FIN AF: 0.718

Gnomad4 NFE AF: 0.700

Gnomad4 OTH AF: 0.727

Alfa AF: 0.701 Hom.: 7812

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1535891; hg19: chr13-43441333;