10-107895095-C-T

Variant names:

• chr10-107895095-C-T
• rs7085286
• ENST00000425050.5:n.545-23342G>A

Variant summary

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

The ENST00000425050.5(LINC01435):​n.545-23342G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.157 in 151,894 control chromosomes in the GnomAD database, including 1,918 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 0.16 (1918 hom., cov: 32)
• Consequence: LINC01435 ENST00000425050.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.488
• 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=-1.05).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.192 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01435	NR_125760.1	n.544-23342G>A		intron_variant	Intron 4 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01435	ENST00000425050.5	n.545-23342G>A		intron_variant	Intron 4 of 4	3
LINC01435	ENST00000593666.6	n.444-40612G>A		intron_variant	Intron 3 of 4	5
LINC01435	ENST00000594427.5	n.484-21243G>A		intron_variant	Intron 3 of 4	5

Frequencies

GnomAD3 genomes AF: 0.157 AC: 23897 AN: 151776 Hom.: 1914 Cov.: 32

Gnomad AFR AF: 0.126

Gnomad AMI AF: 0.146

Gnomad AMR AF: 0.116

Gnomad ASJ AF: 0.202

Gnomad EAS AF: 0.0601

Gnomad SAS AF: 0.144

Gnomad FIN AF: 0.147

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.194

Gnomad OTH AF: 0.143

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

GnomAD4 genome AF: 0.157 AC: 23913 AN: 151894 Hom.: 1918 Cov.: 32 AF XY: 0.154 AC XY: 11445 AN XY: 74232

African (AFR) AF: 0.126 AC: 5209 AN: 41456

American (AMR) AF: 0.115 AC: 1758 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.202 AC: 698 AN: 3462

East Asian (EAS) AF: 0.0602 AC: 311 AN: 5162

South Asian (SAS) AF: 0.146 AC: 702 AN: 4818

European-Finnish (FIN) AF: 0.147 AC: 1553 AN: 10556

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.194 AC: 13205 AN: 67894

Other (OTH) AF: 0.141 AC: 298 AN: 2108

Alfa AF: 0.134 Hom.: 393

Bravo AF: 0.153

Asia WGS AF: 0.111 AC: 388 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	3.9
DANN	Benign	0.40
PhyloP100		0.49
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs7085286; hg19: chr10-109654853;