rs10885394

Variant names:

• chr10-112949029-T-A
• rs10885394
• ENST00000785200.1:n.1781T>A

Variant summary

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

The ENST00000785200.1(LINC02935):​n.1781T>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.201 in 152,150 control chromosomes in the GnomAD database, including 3,808 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 (3808 hom., cov: 31)
• Consequence: LINC02935 ENST00000785200.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.334
• 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=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.275 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02935	ENST00000785200.1	n.1781T>A		non_coding_transcript_exon_variant	Exon 6 of 6
LINC02935	ENST00000785202.1	n.2071T>A		non_coding_transcript_exon_variant	Exon 7 of 7
LINC02935	ENST00000785203.1	n.1132T>A		non_coding_transcript_exon_variant	Exon 5 of 5
LINC02935	ENST00000785204.1	n.785T>A		non_coding_transcript_exon_variant	Exon 3 of 3

Frequencies

GnomAD3 genomes AF: 0.201 AC: 30515 AN: 152032 Hom.: 3802 Cov.: 31

Gnomad AFR AF: 0.0552

Gnomad AMI AF: 0.373

Gnomad AMR AF: 0.265

Gnomad ASJ AF: 0.235

Gnomad EAS AF: 0.0512

Gnomad SAS AF: 0.179

Gnomad FIN AF: 0.233

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.278

Gnomad OTH AF: 0.223

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

GnomAD4 genome AF: 0.201 AC: 30526 AN: 152150 Hom.: 3808 Cov.: 31 AF XY: 0.198 AC XY: 14761 AN XY: 74370

African (AFR) AF: 0.0552 AC: 2292 AN: 41542

American (AMR) AF: 0.265 AC: 4054 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.235 AC: 816 AN: 3468

East Asian (EAS) AF: 0.0513 AC: 266 AN: 5184

South Asian (SAS) AF: 0.180 AC: 868 AN: 4816

European-Finnish (FIN) AF: 0.233 AC: 2461 AN: 10556

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

European-Non Finnish (NFE) AF: 0.278 AC: 18891 AN: 67976

Other (OTH) AF: 0.223 AC: 471 AN: 2114

Alfa AF: 0.241 Hom.: 640

Bravo AF: 0.194

Asia WGS AF: 0.150 AC: 520 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	4.5
DANN	Benign	0.54
PhyloP100		0.33

Splicing

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

Other links and lift over

dbSNP: rs10885394; hg19: chr10-114708788;