rs1411291

Variant names:

• chr10-107839694-A-T
• rs1411291
• ENST00000593666.6:n.492+14741T>A

Variant summary

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

The ENST00000593666.6(LINC01435):​n.492+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 ENST00000593666.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.828
• Publications: 1 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000593666.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01435	ENST00000593666.6	TSL:5	n.492+14741T>A		intron	N/A
	LINC01435	ENST00000596263.5	TSL:5	n.285-26788T>A		intron	N/A
	LINC01435	ENST00000598903.5	TSL:5	n.363+61315T>A		intron	N/A

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

African (AFR) AF: 0.417 AC: 17235 AN: 41302

American (AMR) AF: 0.529 AC: 8013 AN: 15134

Ashkenazi Jewish (ASJ) AF: 0.544 AC: 1883 AN: 3462

East Asian (EAS) AF: 0.554 AC: 2811 AN: 5078

South Asian (SAS) AF: 0.347 AC: 1675 AN: 4822

European-Finnish (FIN) AF: 0.575 AC: 6062 AN: 10550

Middle Eastern (MID) AF: 0.500 AC: 146 AN: 292

European-Non Finnish (NFE) AF: 0.511 AC: 34502 AN: 67550

Other (OTH) AF: 0.493 AC: 1037 AN: 2102

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.99
DANN	Benign	0.34
PhyloP100		-0.83

Splicing

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

Other links and lift over

dbSNP: rs1411291; hg19: chr10-109599452;