10-85393840-T-A

Variant names:

• chr10-85393840-T-A
• rs11596082
• ENST00000655477.1:n.465-14892A>T

Variant summary

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

The ENST00000655477.1(LINC02647):​n.465-14892A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.49 in 149,882 control chromosomes in the GnomAD database, including 18,154 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 0.49 (18154 hom., cov: 27)
• Consequence: LINC02647 ENST00000655477.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.43
• 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=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.555 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.465-14892A>T		intron_variant	Intron 2 of 3
LINC02647	ENST00000658106.1	n.374-14892A>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.490 AC: 73433 AN: 149774 Hom.: 18123 Cov.: 27

Gnomad AFR AF: 0.560

Gnomad AMI AF: 0.366

Gnomad AMR AF: 0.476

Gnomad ASJ AF: 0.550

Gnomad EAS AF: 0.423

Gnomad SAS AF: 0.388

Gnomad FIN AF: 0.476

Gnomad MID AF: 0.557

Gnomad NFE AF: 0.463

Gnomad OTH AF: 0.500

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

GnomAD4 genome AF: 0.490 AC: 73500 AN: 149882 Hom.: 18154 Cov.: 27 AF XY: 0.490 AC XY: 35809 AN XY: 73150

African (AFR) AF: 0.561 AC: 22969 AN: 40958

American (AMR) AF: 0.476 AC: 7152 AN: 15038

Ashkenazi Jewish (ASJ) AF: 0.550 AC: 1897 AN: 3450

East Asian (EAS) AF: 0.423 AC: 2151 AN: 5080

South Asian (SAS) AF: 0.386 AC: 1834 AN: 4750

European-Finnish (FIN) AF: 0.476 AC: 4755 AN: 9990

Middle Eastern (MID) AF: 0.568 AC: 166 AN: 292

European-Non Finnish (NFE) AF: 0.463 AC: 31202 AN: 67344

Other (OTH) AF: 0.502 AC: 1043 AN: 2076

Alfa AF: 0.468 Hom.: 2071

Bravo AF: 0.497

Asia WGS AF: 0.444 AC: 1544 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.83
DANN	Benign	0.63
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs11596082; hg19: chr10-87153596;