chr10-107866308-G-A

Variant names:

• chr10-107866308-G-A
• rs1834180
• ENST00000593666.6:n.444-11825C>T

Variant summary

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

The ENST00000593666.6(LINC01435):​n.444-11825C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.733 in 151,672 control chromosomes in the GnomAD database, including 41,416 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 0.73 (41416 hom., cov: 29)
• Consequence: LINC01435 ENST00000593666.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.371
• Publications: 4 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.909 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01435	ENST00000593666.6	TSL:5	n.444-11825C>T		intron	N/A
	LINC01435	ENST00000594566.5	TSL:5	n.456-21639C>T		intron	N/A
	LINC01435	ENST00000596263.5	TSL:5	n.285-53402C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.733 AC: 111093 AN: 151554 Hom.: 41351 Cov.: 29

Gnomad AFR AF: 0.840

Gnomad AMI AF: 0.649

Gnomad AMR AF: 0.754

Gnomad ASJ AF: 0.700

Gnomad EAS AF: 0.931

Gnomad SAS AF: 0.784

Gnomad FIN AF: 0.612

Gnomad MID AF: 0.709

Gnomad NFE AF: 0.667

Gnomad OTH AF: 0.706

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

GnomAD4 genome AF: 0.733 AC: 111218 AN: 151672 Hom.: 41416 Cov.: 29 AF XY: 0.734 AC XY: 54373 AN XY: 74046

African (AFR) AF: 0.840 AC: 34796 AN: 41406

American (AMR) AF: 0.754 AC: 11458 AN: 15192

Ashkenazi Jewish (ASJ) AF: 0.700 AC: 2427 AN: 3468

East Asian (EAS) AF: 0.931 AC: 4777 AN: 5132

South Asian (SAS) AF: 0.784 AC: 3770 AN: 4810

European-Finnish (FIN) AF: 0.612 AC: 6393 AN: 10448

Middle Eastern (MID) AF: 0.711 AC: 209 AN: 294

European-Non Finnish (NFE) AF: 0.667 AC: 45304 AN: 67900

Other (OTH) AF: 0.707 AC: 1492 AN: 2110

Alfa AF: 0.723 Hom.: 12394

Bravo AF: 0.747

Asia WGS AF: 0.845 AC: 2940 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.1
DANN	Benign	0.27
PhyloP100		0.37

Splicing

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

Other links and lift over

dbSNP: rs1834180; hg19: chr10-109626066;