10-62636035-T-C

Variant names:

• chr10-62636035-T-C
• rs10740085
• ENST00000647733.1:c.1129+12785T>C

Variant summary

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

The ENST00000647733.1(ENSG00000285837):​c.1129+12785T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.847 in 152,254 control chromosomes in the GnomAD database, including 55,063 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 0.85 (55063 hom., cov: 33)
• Consequence: ENSG00000285837 ENST00000647733.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.22
• Publications: 9 publications found

Genes affected

ENSG00000285837 (HGNC:):

LINC02929 (HGNC:55812): (long intergenic non-protein coding RNA 2929)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.952 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000647733.1. 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
	ENSG00000285837	ENST00000647733.1		c.1129+12785T>C		intron	N/A	ENSP00000502188.1
	LINC02929	ENST00000395251.5	TSL:1	n.151-7707T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.847 AC: 128811 AN: 152136 Hom.: 55000 Cov.: 33

Gnomad AFR AF: 0.960

Gnomad AMI AF: 0.855

Gnomad AMR AF: 0.838

Gnomad ASJ AF: 0.800

Gnomad EAS AF: 0.911

Gnomad SAS AF: 0.887

Gnomad FIN AF: 0.806

Gnomad MID AF: 0.712

Gnomad NFE AF: 0.782

Gnomad OTH AF: 0.823

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

GnomAD4 genome AF: 0.847 AC: 128933 AN: 152254 Hom.: 55063 Cov.: 33 AF XY: 0.849 AC XY: 63187 AN XY: 74444

African (AFR) AF: 0.960 AC: 39875 AN: 41552

American (AMR) AF: 0.838 AC: 12827 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.800 AC: 2775 AN: 3470

East Asian (EAS) AF: 0.912 AC: 4722 AN: 5180

South Asian (SAS) AF: 0.887 AC: 4280 AN: 4824

European-Finnish (FIN) AF: 0.806 AC: 8552 AN: 10604

Middle Eastern (MID) AF: 0.707 AC: 208 AN: 294

European-Non Finnish (NFE) AF: 0.782 AC: 53184 AN: 68004

Other (OTH) AF: 0.819 AC: 1732 AN: 2114

Alfa AF: 0.796 Hom.: 41468

Bravo AF: 0.854

Asia WGS AF: 0.876 AC: 3047 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.12
DANN	Benign	0.47
PhyloP100		-2.2
Mutation Taster		=100/0	polymorphism (auto)

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: rs10740085;

hg19: chr10-64395795;