rs1556014

Positions:

• chr10-112894438-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000428766.2(LINC02935):​n.180+3366T>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.253 in 152,060 control chromosomes in the GnomAD database, including 5,291 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 0.25 (5291 hom., cov: 31)
• Consequence: LINC02935 ENST00000428766.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.839

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.293 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC02935	XR_001747706.2	n.41+3366T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02935	ENST00000428766.2	n.180+3366T>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.253 AC: 38510 AN: 151946 Hom.: 5291 Cov.: 31

Gnomad AFR AF: 0.209

Gnomad AMI AF: 0.299

Gnomad AMR AF: 0.228

Gnomad ASJ AF: 0.333

Gnomad EAS AF: 0.00212

Gnomad SAS AF: 0.195

Gnomad FIN AF: 0.298

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.297

Gnomad OTH AF: 0.288

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

GnomAD4 genome AF: 0.253 AC: 38521 AN: 152060 Hom.: 5291 Cov.: 31 AF XY: 0.252 AC XY: 18711 AN XY: 74308

Gnomad4 AFR AF: 0.208

Gnomad4 AMR AF: 0.228

Gnomad4 ASJ AF: 0.333

Gnomad4 EAS AF: 0.00212

Gnomad4 SAS AF: 0.196

Gnomad4 FIN AF: 0.298

Gnomad4 NFE AF: 0.297

Gnomad4 OTH AF: 0.286

Alfa AF: 0.269 Hom.: 2284

Bravo AF: 0.245

Asia WGS AF: 0.0830 AC: 289 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.4
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1556014; hg19: chr10-114654197;