ENST00000647733.1:c.981+66659A>C

Variant names:

• chr10-62526456-A-C
• rs7082733
• ENST00000647733.1:c.981+66659A>C

Variant summary

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

The ENST00000647733.1(ENSG00000285837):​c.981+66659A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.425 in 151,950 control chromosomes in the GnomAD database, including 14,481 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 0.42 (14481 hom., cov: 31)
• Consequence: ENSG00000285837 ENST00000647733.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.347
• Publications: 2 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=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.567 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.981+66659A>C		intron_variant	Intron 4 of 7			ENSP00000502188.1
LINC02929	ENST00000395251.5	n.150+5859A>C		intron_variant	Intron 1 of 6	1

Frequencies

GnomAD3 genomes AF: 0.424 AC: 64424 AN: 151832 Hom.: 14444 Cov.: 31

Gnomad AFR AF: 0.573

Gnomad AMI AF: 0.366

Gnomad AMR AF: 0.428

Gnomad ASJ AF: 0.371

Gnomad EAS AF: 0.289

Gnomad SAS AF: 0.454

Gnomad FIN AF: 0.310

Gnomad MID AF: 0.399

Gnomad NFE AF: 0.363

Gnomad OTH AF: 0.412

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

GnomAD4 genome AF: 0.425 AC: 64528 AN: 151950 Hom.: 14481 Cov.: 31 AF XY: 0.424 AC XY: 31450 AN XY: 74248

African (AFR) AF: 0.573 AC: 23714 AN: 41390

American (AMR) AF: 0.428 AC: 6547 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.371 AC: 1286 AN: 3466

East Asian (EAS) AF: 0.290 AC: 1487 AN: 5132

South Asian (SAS) AF: 0.457 AC: 2202 AN: 4822

European-Finnish (FIN) AF: 0.310 AC: 3275 AN: 10574

Middle Eastern (MID) AF: 0.415 AC: 122 AN: 294

European-Non Finnish (NFE) AF: 0.363 AC: 24684 AN: 67970

Other (OTH) AF: 0.416 AC: 877 AN: 2108

Alfa AF: 0.212 Hom.: 399

Bravo AF: 0.438

Asia WGS AF: 0.388 AC: 1348 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.0
DANN	Benign	0.73
PhyloP100		0.35
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: rs7082733; hg19: chr10-64286215;