10-112933374-G-A

Variant names:

• chr10-112933374-G-A
• rs10885392
• ENST00000428766.3:n.420-7705G>A

Variant summary

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

The ENST00000428766.3(LINC02935):​n.420-7705G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.218 in 151,796 control chromosomes in the GnomAD database, including 4,028 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 0.22 (4028 hom., cov: 32)
• Consequence: LINC02935 ENST00000428766.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.485
• Publications: 3 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=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.271 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000428766.3. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02935	ENST00000428766.3	TSL:5	n.420-7705G>A		intron	N/A
	LINC02935	ENST00000785198.1		n.418-10885G>A		intron	N/A
	LINC02935	ENST00000785199.1		n.189-7705G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.218 AC: 33043 AN: 151678 Hom.: 4023 Cov.: 32

Gnomad AFR AF: 0.107

Gnomad AMI AF: 0.372

Gnomad AMR AF: 0.274

Gnomad ASJ AF: 0.206

Gnomad EAS AF: 0.0634

Gnomad SAS AF: 0.215

Gnomad FIN AF: 0.273

Gnomad MID AF: 0.223

Gnomad NFE AF: 0.274

Gnomad OTH AF: 0.223

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

GnomAD4 genome AF: 0.218 AC: 33058 AN: 151796 Hom.: 4028 Cov.: 32 AF XY: 0.217 AC XY: 16089 AN XY: 74162

African (AFR) AF: 0.107 AC: 4431 AN: 41376

American (AMR) AF: 0.274 AC: 4188 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.206 AC: 716 AN: 3470

East Asian (EAS) AF: 0.0637 AC: 329 AN: 5162

South Asian (SAS) AF: 0.215 AC: 1032 AN: 4806

European-Finnish (FIN) AF: 0.273 AC: 2865 AN: 10496

Middle Eastern (MID) AF: 0.226 AC: 66 AN: 292

European-Non Finnish (NFE) AF: 0.274 AC: 18622 AN: 67918

Other (OTH) AF: 0.224 AC: 472 AN: 2110

Alfa AF: 0.236 Hom.: 1960

Bravo AF: 0.211

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.5
DANN	Benign	0.56
PhyloP100		0.48

Splicing

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

Other links and lift over

dbSNP: rs10885392; hg19: chr10-114693133;