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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105378327	XR_946002.3	n.161-10912A>G		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000285837	ENST00000647733.1	c.1129+12785T>C		intron_variant	Intron 5 of 7			ENSP00000502188.1
LINC02929	ENST00000395251.5	n.151-7707T>C		intron_variant	Intron 1 of 6	1

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 v4.3

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

Other links and lift over

dbSNP: rs10740085; hg19: chr10-64395795;