rs1556014

Variant names:

• chr10-112894438-T-C
• rs1556014
• ENST00000428766.3:n.182+3366T>C

Variant summary

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

The ENST00000785198.1(LINC02935):​n.180+3366T>C variant causes a intron 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 ENST00000785198.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.839
• Publications: 4 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 (NFE) allele frequency at 95% confidence interval = 0.293 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000785198.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02935	ENST00000428766.3	TSL:5	n.182+3366T>C		intron	N/A
	LINC02935	ENST00000785198.1		n.180+3366T>C		intron	N/A
	LINC02935	ENST00000785199.1		n.188+3366T>C		intron	N/A

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

African (AFR) AF: 0.208 AC: 8639 AN: 41466

American (AMR) AF: 0.228 AC: 3478 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.333 AC: 1157 AN: 3472

East Asian (EAS) AF: 0.00212 AC: 11 AN: 5188

South Asian (SAS) AF: 0.196 AC: 942 AN: 4818

European-Finnish (FIN) AF: 0.298 AC: 3147 AN: 10558

Middle Eastern (MID) AF: 0.330 AC: 97 AN: 294

European-Non Finnish (NFE) AF: 0.297 AC: 20176 AN: 67980

Other (OTH) AF: 0.286 AC: 602 AN: 2108

Alfa AF: 0.271 Hom.: 2809

Bravo AF: 0.245

Asia WGS AF: 0.0830 AC: 289 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.4
DANN	Benign	0.75
PhyloP100		-0.84

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1556014;

hg19: chr10-114654197;