chr10-112949509-C-T

Variant names:

• chr10-112949509-C-T
• rs10885395
• ENST00000785200.1:n.*108C>T

Variant summary

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

The ENST00000785200.1(LINC02935):​n.*108C>T variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.201 in 151,974 control chromosomes in the GnomAD database, including 3,795 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 0.20 (3795 hom., cov: 31)
• Consequence: LINC02935 ENST00000785200.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.597
• Publications: 5 publications found

Genes affected

LINC02935 (HGNC:55939): (long intergenic non-protein coding RNA 2935)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.51).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.274 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000785200.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02935	ENST00000785200.1		n.*108C>T		downstream_gene	N/A
	LINC02935	ENST00000785202.1		n.*108C>T		downstream_gene	N/A
	LINC02935	ENST00000785203.1		n.*108C>T		downstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.201 AC: 30491 AN: 151860 Hom.: 3789 Cov.: 31

Gnomad AFR AF: 0.0553

Gnomad AMI AF: 0.370

Gnomad AMR AF: 0.266

Gnomad ASJ AF: 0.235

Gnomad EAS AF: 0.0515

Gnomad SAS AF: 0.179

Gnomad FIN AF: 0.234

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.278

Gnomad OTH AF: 0.222

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

GnomAD4 genome AF: 0.201 AC: 30502 AN: 151974 Hom.: 3795 Cov.: 31 AF XY: 0.199 AC XY: 14743 AN XY: 74260

African (AFR) AF: 0.0553 AC: 2293 AN: 41468

American (AMR) AF: 0.266 AC: 4060 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.235 AC: 816 AN: 3470

East Asian (EAS) AF: 0.0516 AC: 267 AN: 5176

South Asian (SAS) AF: 0.180 AC: 864 AN: 4812

European-Finnish (FIN) AF: 0.234 AC: 2458 AN: 10514

Middle Eastern (MID) AF: 0.231 AC: 68 AN: 294

European-Non Finnish (NFE) AF: 0.278 AC: 18872 AN: 67946

Other (OTH) AF: 0.222 AC: 467 AN: 2106

Alfa AF: 0.230 Hom.: 1518

Bravo AF: 0.194

Asia WGS AF: 0.150 AC: 521 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.51
CADD	Benign	9.1
DANN	Benign	0.58
PhyloP100		0.60

Splicing

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

Other links and lift over

dbSNP: rs10885395; hg19: chr10-114709268;