chr10-112948751-C-T

Variant names:

• chr10-112948751-C-T
• rs3814570
• ENST00000785200.1:n.1503C>T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000785200.1(LINC02935):​n.1503C>T 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 0.227 in 151,982 control chromosomes in the GnomAD database, including 4,391 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 (4391 hom., cov: 31)
• Consequence: LINC02935 ENST00000785200.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.96
• Publications: 17 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.22).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.285 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.1503C>T		non_coding_transcript_exon_variant	Exon 6 of 6
LINC02935	ENST00000785202.1	n.1793C>T		non_coding_transcript_exon_variant	Exon 7 of 7
LINC02935	ENST00000785203.1	n.1039-185C>T		intron_variant	Intron 4 of 4
LINC02935	ENST00000785204.1	n.692-185C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.227 AC: 34412 AN: 151864 Hom.: 4386 Cov.: 31

Gnomad AFR AF: 0.109

Gnomad AMI AF: 0.373

Gnomad AMR AF: 0.289

Gnomad ASJ AF: 0.239

Gnomad EAS AF: 0.0646

Gnomad SAS AF: 0.193

Gnomad FIN AF: 0.274

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.288

Gnomad OTH AF: 0.245

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

GnomAD4 genome AF: 0.227 AC: 34434 AN: 151982 Hom.: 4391 Cov.: 31 AF XY: 0.225 AC XY: 16735 AN XY: 74282

African (AFR) AF: 0.109 AC: 4517 AN: 41456

American (AMR) AF: 0.289 AC: 4411 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.239 AC: 829 AN: 3472

East Asian (EAS) AF: 0.0650 AC: 336 AN: 5172

South Asian (SAS) AF: 0.194 AC: 930 AN: 4806

European-Finnish (FIN) AF: 0.274 AC: 2887 AN: 10534

Middle Eastern (MID) AF: 0.235 AC: 69 AN: 294

European-Non Finnish (NFE) AF: 0.288 AC: 19601 AN: 67960

Other (OTH) AF: 0.245 AC: 515 AN: 2106

Alfa AF: 0.265 Hom.: 19704

Bravo AF: 0.221

Asia WGS AF: 0.172 AC: 597 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.22
CADD	Benign	15
DANN	Benign	0.67
PhyloP100		2.0

Splicing

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

Other links and lift over

dbSNP: rs3814570; hg19: chr10-114708510;