10-85397533-C-T

Variant names:

• chr10-85397533-C-T
• rs2351337
• ENST00000655477.1:n.465-18585G>A

Variant summary

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

The ENST00000655477.1(LINC02647):​n.465-18585G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.48 in 151,896 control chromosomes in the GnomAD database, including 17,583 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 0.48 (17583 hom., cov: 33)
• Consequence: LINC02647 ENST00000655477.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.221
• Publications: 1 publications found

Genes affected

LINC02647 (HGNC:54131): (long intergenic non-protein coding RNA 2647)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.524 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
LINC02647	ENST00000655477.1	n.465-18585G>A		intron_variant	Intron 2 of 3
LINC02647	ENST00000658106.1	n.374-18585G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.480 AC: 72824 AN: 151778 Hom.: 17559 Cov.: 33

Gnomad AFR AF: 0.529

Gnomad AMI AF: 0.365

Gnomad AMR AF: 0.472

Gnomad ASJ AF: 0.549

Gnomad EAS AF: 0.421

Gnomad SAS AF: 0.387

Gnomad FIN AF: 0.468

Gnomad MID AF: 0.561

Gnomad NFE AF: 0.462

Gnomad OTH AF: 0.489

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

GnomAD4 genome AF: 0.480 AC: 72885 AN: 151896 Hom.: 17583 Cov.: 33 AF XY: 0.479 AC XY: 35578 AN XY: 74238

African (AFR) AF: 0.530 AC: 21947 AN: 41436

American (AMR) AF: 0.471 AC: 7185 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.549 AC: 1904 AN: 3468

East Asian (EAS) AF: 0.421 AC: 2162 AN: 5138

South Asian (SAS) AF: 0.385 AC: 1855 AN: 4820

European-Finnish (FIN) AF: 0.468 AC: 4940 AN: 10560

Middle Eastern (MID) AF: 0.572 AC: 166 AN: 290

European-Non Finnish (NFE) AF: 0.462 AC: 31358 AN: 67914

Other (OTH) AF: 0.491 AC: 1035 AN: 2110

Alfa AF: 0.376 Hom.: 1516

Bravo AF: 0.488

Asia WGS AF: 0.442 AC: 1541 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.9
DANN	Benign	0.45
PhyloP100		-0.22

Splicing

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

Other links and lift over

dbSNP: rs2351337; hg19: chr10-87157289;