10-62646598-C-G

Variant names:

• chr10-62646598-C-G
• rs12768538
• ENST00000647733.1:c.1130-9798C>G

Variant summary

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

The ENST00000647733.1(ENSG00000285837):​c.1130-9798C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.295 in 151,978 control chromosomes in the GnomAD database, including 7,949 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 0.30 (7949 hom., cov: 31)
• Consequence: ENSG00000285837 ENST00000647733.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.697
• Publications: 5 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=-0.72).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.571 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.1130-9798C>G		intron	N/A	ENSP00000502188.1
	LINC02929	ENST00000344640.7	TSL:1	n.191+2635C>G		intron	N/A
	LINC02929	ENST00000373784.6	TSL:1	n.191+2635C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.296 AC: 44906 AN: 151862 Hom.: 7953 Cov.: 31

Gnomad AFR AF: 0.117

Gnomad AMI AF: 0.450

Gnomad AMR AF: 0.220

Gnomad ASJ AF: 0.395

Gnomad EAS AF: 0.588

Gnomad SAS AF: 0.383

Gnomad FIN AF: 0.366

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.375

Gnomad OTH AF: 0.295

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

GnomAD4 genome AF: 0.295 AC: 44889 AN: 151978 Hom.: 7949 Cov.: 31 AF XY: 0.297 AC XY: 22030 AN XY: 74260

African (AFR) AF: 0.117 AC: 4857 AN: 41470

American (AMR) AF: 0.220 AC: 3358 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.395 AC: 1371 AN: 3472

East Asian (EAS) AF: 0.588 AC: 3035 AN: 5158

South Asian (SAS) AF: 0.382 AC: 1835 AN: 4808

European-Finnish (FIN) AF: 0.366 AC: 3864 AN: 10546

Middle Eastern (MID) AF: 0.316 AC: 93 AN: 294

European-Non Finnish (NFE) AF: 0.375 AC: 25451 AN: 67942

Other (OTH) AF: 0.292 AC: 616 AN: 2112

Alfa AF: 0.312 Hom.: 999

Bravo AF: 0.275

Asia WGS AF: 0.410 AC: 1426 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	1.3
DANN	Benign	0.82
PhyloP100		-0.70
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: rs12768538;

hg19: chr10-64406358;