chr10-16280711-A-G

Variant names:

• chr10-16280711-A-G
• rs7075260
• ENST00000417542.1:n.49+1962A>G

Variant summary

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

The ENST00000417542.1(LINC02654):​n.49+1962A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.454 in 152,164 control chromosomes in the GnomAD database, including 19,511 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 0.45 (19511 hom., cov: 32)
• Consequence: LINC02654 ENST00000417542.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.854
• Publications: 1 publications found

Genes affected

LINC02654 (HGNC:54140): (long intergenic non-protein coding RNA 2654)

ENSG00000295551 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.612 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02654	NR_184073.1	n.693+1962A>G		intron_variant	Intron 1 of 2
LINC02654	NR_184074.1	n.693+1962A>G		intron_variant	Intron 1 of 2
LINC02654	NR_184075.1	n.693+1962A>G		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02654	ENST00000417542.1	n.49+1962A>G		intron_variant	Intron 1 of 3	2
LINC02654	ENST00000434386.6	n.206+1962A>G		intron_variant	Intron 2 of 3	2
LINC02654	ENST00000652949.1	n.657+1962A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.455 AC: 69129 AN: 152046 Hom.: 19506 Cov.: 32

Gnomad AFR AF: 0.140

Gnomad AMI AF: 0.553

Gnomad AMR AF: 0.565

Gnomad ASJ AF: 0.641

Gnomad EAS AF: 0.115

Gnomad SAS AF: 0.285

Gnomad FIN AF: 0.652

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.617

Gnomad OTH AF: 0.496

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

GnomAD4 genome AF: 0.454 AC: 69134 AN: 152164 Hom.: 19511 Cov.: 32 AF XY: 0.452 AC XY: 33630 AN XY: 74384

African (AFR) AF: 0.139 AC: 5782 AN: 41538

American (AMR) AF: 0.565 AC: 8642 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.641 AC: 2225 AN: 3472

East Asian (EAS) AF: 0.115 AC: 594 AN: 5180

South Asian (SAS) AF: 0.284 AC: 1368 AN: 4818

European-Finnish (FIN) AF: 0.652 AC: 6887 AN: 10568

Middle Eastern (MID) AF: 0.541 AC: 159 AN: 294

European-Non Finnish (NFE) AF: 0.617 AC: 41939 AN: 67990

Other (OTH) AF: 0.491 AC: 1036 AN: 2110

Alfa AF: 0.563 Hom.: 36899

Bravo AF: 0.440

Asia WGS AF: 0.202 AC: 703 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.060
DANN	Benign	0.66
PhyloP100		-0.85

Splicing

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

Other links and lift over

dbSNP: rs7075260; hg19: chr10-16322710;