10-107895095-C-T

Position:

• chr10-107895095-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_125760.1(LINC01435):​n.544-23342G>A variant causes a intron, non coding transcript 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 NR_125760.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.488

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
LINC01435	NR_125760.1	n.544-23342G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01435	ENST00000630847.2	n.273+5914G>A		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.126

Gnomad4 AMR AF: 0.115

Gnomad4 ASJ AF: 0.202

Gnomad4 EAS AF: 0.0602

Gnomad4 SAS AF: 0.146

Gnomad4 FIN AF: 0.147

Gnomad4 NFE AF: 0.194

Gnomad4 OTH AF: 0.141

Alfa AF: 0.133 Hom.: 366

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7085286; hg19: chr10-109654853;