rs1411291

Variant names:

• chr10-107839694-A-T
• rs1411291
• ENST00000593666.5:n.333+14741T>A

Variant summary

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

The ENST00000593666.5(LINC01435):​n.333+14741T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.489 in 151,204 control chromosomes in the GnomAD database, including 18,328 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 0.49 (18328 hom., cov: 31)
• Consequence: LINC01435 ENST00000593666.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.828

Genes affected

LINC01435 (HGNC:50753): (long intergenic non-protein coding RNA 1435)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.537 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01435	ENST00000593666.5	n.333+14741T>A		intron_variant	Intron 3 of 3	5
LINC01435	ENST00000596263.5	n.285-26788T>A		intron_variant	Intron 2 of 3	5
LINC01435	ENST00000598903.5	n.363+61315T>A		intron_variant	Intron 3 of 4	5
LINC01435	ENST00000630847.2	n.525+13464T>A		intron_variant	Intron 5 of 5	5

Frequencies

GnomAD3 genomes AF: 0.488 AC: 73806 AN: 151088 Hom.: 18289 Cov.: 31

Gnomad AFR AF: 0.417

Gnomad AMI AF: 0.593

Gnomad AMR AF: 0.528

Gnomad ASJ AF: 0.544

Gnomad EAS AF: 0.555

Gnomad SAS AF: 0.347

Gnomad FIN AF: 0.575

Gnomad MID AF: 0.510

Gnomad NFE AF: 0.511

Gnomad OTH AF: 0.487

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

GnomAD4 genome AF: 0.489 AC: 73905 AN: 151204 Hom.: 18328 Cov.: 31 AF XY: 0.489 AC XY: 36142 AN XY: 73854

Gnomad4 AFR AF: 0.417

Gnomad4 AMR AF: 0.529

Gnomad4 ASJ AF: 0.544

Gnomad4 EAS AF: 0.554

Gnomad4 SAS AF: 0.347

Gnomad4 FIN AF: 0.575

Gnomad4 NFE AF: 0.511

Gnomad4 OTH AF: 0.493

Alfa AF: 0.511 Hom.: 2504

Bravo AF: 0.489

Asia WGS AF: 0.465 AC: 1622 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.99
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1411291; hg19: chr10-109599452;