rs9332405

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr10-108428634-T-A
• chr10-108428634-T-C
• chr10-108428634-T-G

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000809134.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01435	ENST00000809134.1		n.158+1088A>T		intron	N/A
	LINC01435	ENST00000809136.1		n.540+21336A>T		intron	N/A
	LINC01435	ENST00000809137.1		n.541-7152A>T		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs9332405;

hg19: chr10-110188392;