10-108428634-T-A

Variant names:

• chr10-108428634-T-A
• rs9332405
• ENST00000809134.1:n.158+1088A>T

Variant summary

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

The ENST00000809134.1(LINC01435):​n.158+1088A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.299 in 151,958 control chromosomes in the GnomAD database, including 7,877 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 0.30 (7877 hom., cov: 31)
• Consequence: LINC01435 ENST00000809134.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.35
• Publications: 3 publications found

Genes affected

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

LOC105378477 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.651 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105378477	XR_946308.2	n.911+21336A>T		intron_variant	Intron 3 of 4
LOC105378477	XR_946309.2	n.634+21336A>T		intron_variant	Intron 3 of 4
LOC105378477	XR_946310.2	n.613+21336A>T		intron_variant	Intron 3 of 4
LOC105378477	XR_946312.2	n.912-7152A>T		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01435	ENST00000809134.1	n.158+1088A>T		intron_variant	Intron 1 of 3
LINC01435	ENST00000809136.1	n.540+21336A>T		intron_variant	Intron 3 of 4
LINC01435	ENST00000809137.1	n.541-7152A>T		intron_variant	Intron 3 of 3
LINC01435	ENST00000809138.1	n.144+1088A>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.299 AC: 45370 AN: 151840 Hom.: 7854 Cov.: 31

Gnomad AFR AF: 0.160

Gnomad AMI AF: 0.338

Gnomad AMR AF: 0.460

Gnomad ASJ AF: 0.330

Gnomad EAS AF: 0.670

Gnomad SAS AF: 0.423

Gnomad FIN AF: 0.337

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.302

Gnomad OTH AF: 0.290

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

GnomAD4 genome AF: 0.299 AC: 45409 AN: 151958 Hom.: 7877 Cov.: 31 AF XY: 0.307 AC XY: 22787 AN XY: 74268

African (AFR) AF: 0.160 AC: 6620 AN: 41440

American (AMR) AF: 0.461 AC: 7042 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.330 AC: 1144 AN: 3468

East Asian (EAS) AF: 0.670 AC: 3447 AN: 5146

South Asian (SAS) AF: 0.422 AC: 2027 AN: 4802

European-Finnish (FIN) AF: 0.337 AC: 3564 AN: 10562

Middle Eastern (MID) AF: 0.279 AC: 82 AN: 294

European-Non Finnish (NFE) AF: 0.302 AC: 20551 AN: 67964

Other (OTH) AF: 0.296 AC: 624 AN: 2106

Alfa AF: 0.301 Hom.: 902

Bravo AF: 0.306

Asia WGS AF: 0.511 AC: 1778 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.8
DANN	Benign	0.41
PhyloP100		1.4

Splicing

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

Other links and lift over

dbSNP: rs9332405; hg19: chr10-110188392;