chr10-2489827-G-C

Variant names:

• chr10-2489827-G-C
• rs729397
• ENST00000773612.1:n.439C>G

Variant summary

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

The ENST00000773612.1(LINC02645):​n.439C>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.256 in 152,146 control chromosomes in the GnomAD database, including 5,182 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 0.26 (5182 hom., cov: 32)
• Consequence: LINC02645 ENST00000773612.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.232
• Publications: 6 publications found

Genes affected

LINC02645 (HGNC:54129): (long intergenic non-protein coding RNA 2645)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.283 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02645	NR_136146.1	n.89+11547C>G		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02645	ENST00000773612.1	n.439C>G		non_coding_transcript_exon_variant	Exon 2 of 2
LINC02645	ENST00000773613.1	n.516C>G		non_coding_transcript_exon_variant	Exon 2 of 2
LINC02645	ENST00000773614.1	n.380C>G		non_coding_transcript_exon_variant	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.256 AC: 38940 AN: 152028 Hom.: 5177 Cov.: 32

Gnomad AFR AF: 0.278

Gnomad AMI AF: 0.348

Gnomad AMR AF: 0.215

Gnomad ASJ AF: 0.278

Gnomad EAS AF: 0.0638

Gnomad SAS AF: 0.191

Gnomad FIN AF: 0.144

Gnomad MID AF: 0.309

Gnomad NFE AF: 0.286

Gnomad OTH AF: 0.262

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

GnomAD4 genome AF: 0.256 AC: 38971 AN: 152146 Hom.: 5182 Cov.: 32 AF XY: 0.245 AC XY: 18198 AN XY: 74380

African (AFR) AF: 0.278 AC: 11521 AN: 41496

American (AMR) AF: 0.215 AC: 3280 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.278 AC: 962 AN: 3466

East Asian (EAS) AF: 0.0637 AC: 329 AN: 5164

South Asian (SAS) AF: 0.193 AC: 929 AN: 4822

European-Finnish (FIN) AF: 0.144 AC: 1529 AN: 10616

Middle Eastern (MID) AF: 0.301 AC: 88 AN: 292

European-Non Finnish (NFE) AF: 0.286 AC: 19456 AN: 67988

Other (OTH) AF: 0.265 AC: 560 AN: 2112

Alfa AF: 0.155 Hom.: 262

Bravo AF: 0.261

Asia WGS AF: 0.150 AC: 523 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.2
DANN	Benign	0.42
PhyloP100		-0.23

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs729397; hg19: chr10-2532019;