10-108102097-C-T

Position:

• chr10-108102097-C-T

Variant summary

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

The ENST00000600953.3(LINC01435):​n.106+9400G>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 0.234 in 151,600 control chromosomes in the GnomAD database, including 4,350 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 0.23 (4350 hom., cov: 31)
• Consequence: LINC01435 ENST00000600953.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.339

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=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.251 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01435	ENST00000600953.3	n.106+9400G>A		intron_variant, non_coding_transcript_variant		5
LINC01435	ENST00000627225.2	n.270+9400G>A		intron_variant, non_coding_transcript_variant		5
LINC01435	ENST00000629275.2	n.220+9400G>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.234 AC: 35499 AN: 151494 Hom.: 4349 Cov.: 31

Gnomad AFR AF: 0.256

Gnomad AMI AF: 0.107

Gnomad AMR AF: 0.253

Gnomad ASJ AF: 0.243

Gnomad EAS AF: 0.101

Gnomad SAS AF: 0.197

Gnomad FIN AF: 0.153

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.244

Gnomad OTH AF: 0.225

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

GnomAD4 genome AF: 0.234 AC: 35519 AN: 151600 Hom.: 4350 Cov.: 31 AF XY: 0.230 AC XY: 17045 AN XY: 74034

Gnomad4 AFR AF: 0.256

Gnomad4 AMR AF: 0.253

Gnomad4 ASJ AF: 0.243

Gnomad4 EAS AF: 0.101

Gnomad4 SAS AF: 0.198

Gnomad4 FIN AF: 0.153

Gnomad4 NFE AF: 0.244

Gnomad4 OTH AF: 0.222

Alfa AF: 0.241 Hom.: 5757

Bravo AF: 0.240

Asia WGS AF: 0.141 AC: 494 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.20
DANN	Benign	0.15

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1931600; hg19: chr10-109861855;