chr10-108030075-G-T

Variant names:

• chr10-108030075-G-T
• rs1931605
• ENST00000425050.5:n.544+10286C>A

Variant summary

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

The ENST00000425050.5(LINC01435):​n.544+10286C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.527 in 151,960 control chromosomes in the GnomAD database, including 23,712 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 0.53 (23712 hom., cov: 32)
• Consequence: LINC01435 ENST00000425050.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.09
• Publications: 2 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=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.803 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000425050.5. 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
	LINC01435	NR_125760.1		n.543+10286C>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01435	ENST00000425050.5	TSL:3	n.544+10286C>A		intron	N/A
	LINC01435	ENST00000593666.6	TSL:5	n.443+10286C>A		intron	N/A
	LINC01435	ENST00000594427.5	TSL:5	n.284+10286C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.527 AC: 80029 AN: 151842 Hom.: 23652 Cov.: 32

Gnomad AFR AF: 0.810

Gnomad AMI AF: 0.376

Gnomad AMR AF: 0.454

Gnomad ASJ AF: 0.580

Gnomad EAS AF: 0.216

Gnomad SAS AF: 0.362

Gnomad FIN AF: 0.325

Gnomad MID AF: 0.582

Gnomad NFE AF: 0.438

Gnomad OTH AF: 0.513

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

GnomAD4 genome AF: 0.527 AC: 80133 AN: 151960 Hom.: 23712 Cov.: 32 AF XY: 0.519 AC XY: 38509 AN XY: 74258

African (AFR) AF: 0.810 AC: 33590 AN: 41466

American (AMR) AF: 0.453 AC: 6904 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.580 AC: 2011 AN: 3466

East Asian (EAS) AF: 0.216 AC: 1118 AN: 5170

South Asian (SAS) AF: 0.363 AC: 1748 AN: 4818

European-Finnish (FIN) AF: 0.325 AC: 3429 AN: 10542

Middle Eastern (MID) AF: 0.588 AC: 173 AN: 294

European-Non Finnish (NFE) AF: 0.438 AC: 29752 AN: 67950

Other (OTH) AF: 0.507 AC: 1067 AN: 2104

Alfa AF: 0.502 Hom.: 3237

Bravo AF: 0.548

Asia WGS AF: 0.323 AC: 1128 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.48
DANN	Benign	0.12
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs1931605; hg19: chr10-109789833;