10-108102097-C-T

Variant names:

• chr10-108102097-C-T
• rs1931600
• ENST00000600953.3:n.106+9400G>A

Variant summary

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

The ENST00000659061.1(LINC01435):​n.4+9400G>A variant causes a intron 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 ENST00000659061.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.339
• 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=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.251 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000659061.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01435	ENST00000600953.3	TSL:5	n.106+9400G>A		intron	N/A
	LINC01435	ENST00000627225.2	TSL:5	n.270+9400G>A		intron	N/A
	LINC01435	ENST00000629275.2	TSL:5	n.220+9400G>A		intron	N/A

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

African (AFR) AF: 0.256 AC: 10568 AN: 41354

American (AMR) AF: 0.253 AC: 3857 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.243 AC: 842 AN: 3464

East Asian (EAS) AF: 0.101 AC: 522 AN: 5152

South Asian (SAS) AF: 0.198 AC: 954 AN: 4822

European-Finnish (FIN) AF: 0.153 AC: 1590 AN: 10408

Middle Eastern (MID) AF: 0.323 AC: 95 AN: 294

European-Non Finnish (NFE) AF: 0.244 AC: 16526 AN: 67840

Other (OTH) AF: 0.222 AC: 467 AN: 2108

Alfa AF: 0.242 Hom.: 7352

Bravo AF: 0.240

Asia WGS AF: 0.141 AC: 494 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.20
DANN	Benign	0.15
PhyloP100		-0.34

Splicing

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

Other links and lift over

dbSNP: rs1931600; hg19: chr10-109861855;