10-85397533-C-T

Position:

• chr10-85397533-C-T

Variant summary

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

The ENST00000658106.1(LINC02647):​n.374-18585G>A variant causes a intron, non coding transcript 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 ENST00000658106.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.221

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=-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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02647	ENST00000658106.1	n.374-18585G>A		intron_variant, non_coding_transcript_variant
LINC02647	ENST00000655477.1	n.465-18585G>A		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.530

Gnomad4 AMR AF: 0.471

Gnomad4 ASJ AF: 0.549

Gnomad4 EAS AF: 0.421

Gnomad4 SAS AF: 0.385

Gnomad4 FIN AF: 0.468

Gnomad4 NFE AF: 0.462

Gnomad4 OTH AF: 0.491

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2351337; hg19: chr10-87157289;