chr10-85393883-A-G

Variant names:

• chr10-85393883-A-G
• rs7089868
• ENST00000655477.1:n.465-14935T>C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000655477.1(LINC02647):​n.465-14935T>C 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 150,600 control chromosomes in the GnomAD database, including 17,461 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 (17461 hom., cov: 28)
• Consequence: LINC02647 ENST00000655477.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.479

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• 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.465-14935T>C		intron_variant	Intron 2 of 3
LINC02647	ENST00000658106.1	n.374-14935T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.480 AC: 72219 AN: 150488 Hom.: 17438 Cov.: 28

Gnomad AFR AF: 0.529

Gnomad AMI AF: 0.365

Gnomad AMR AF: 0.471

Gnomad ASJ AF: 0.549

Gnomad EAS AF: 0.421

Gnomad SAS AF: 0.386

Gnomad FIN AF: 0.468

Gnomad MID AF: 0.560

Gnomad NFE AF: 0.462

Gnomad OTH AF: 0.487

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

GnomAD4 genome AF: 0.480 AC: 72276 AN: 150600 Hom.: 17461 Cov.: 28 AF XY: 0.479 AC XY: 35270 AN XY: 73588

Gnomad4 AFR AF: 0.530

Gnomad4 AMR AF: 0.471

Gnomad4 ASJ AF: 0.549

Gnomad4 EAS AF: 0.421

Gnomad4 SAS AF: 0.384

Gnomad4 FIN AF: 0.468

Gnomad4 NFE AF: 0.462

Gnomad4 OTH AF: 0.489

Alfa AF: 0.464 Hom.: 2722

Bravo AF: 0.488

Asia WGS AF: 0.440 AC: 1534 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	3.2
DANN	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7089868; hg19: chr10-87153639;