10-62620576-T-C

Variant names:

• chr10-62620576-T-C
• rs2393903
• ENST00000647733.1:c.982-2527T>C

Variant summary

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

The ENST00000647733.1(ENSG00000285837):​c.982-2527T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.673 in 152,162 control chromosomes in the GnomAD database, including 36,072 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 0.67 (36072 hom., cov: 33)
• Consequence: ENSG00000285837 ENST00000647733.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.02
• Publications: 11 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.868 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
ENSG00000285837	ENST00000647733.1	c.982-2527T>C		intron_variant	Intron 4 of 7			ENSP00000502188.1
LINC02929	ENST00000395251.5	n.151-23166T>C		intron_variant	Intron 1 of 6	1

Frequencies

GnomAD3 genomes AF: 0.673 AC: 102287 AN: 152044 Hom.: 36010 Cov.: 33

Gnomad AFR AF: 0.875

Gnomad AMI AF: 0.579

Gnomad AMR AF: 0.678

Gnomad ASJ AF: 0.540

Gnomad EAS AF: 0.478

Gnomad SAS AF: 0.556

Gnomad FIN AF: 0.723

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.574

Gnomad OTH AF: 0.621

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

GnomAD4 genome AF: 0.673 AC: 102422 AN: 152162 Hom.: 36072 Cov.: 33 AF XY: 0.677 AC XY: 50376 AN XY: 74386

African (AFR) AF: 0.875 AC: 36348 AN: 41528

American (AMR) AF: 0.678 AC: 10376 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.540 AC: 1873 AN: 3466

East Asian (EAS) AF: 0.477 AC: 2468 AN: 5170

South Asian (SAS) AF: 0.557 AC: 2688 AN: 4824

European-Finnish (FIN) AF: 0.723 AC: 7648 AN: 10584

Middle Eastern (MID) AF: 0.435 AC: 128 AN: 294

European-Non Finnish (NFE) AF: 0.574 AC: 39048 AN: 67978

Other (OTH) AF: 0.624 AC: 1317 AN: 2112

Alfa AF: 0.601 Hom.: 107807

Bravo AF: 0.677

Asia WGS AF: 0.597 AC: 2077 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.14
DANN	Benign	0.53
PhyloP100		-3.0
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: rs2393903; hg19: chr10-64380336;