chr10-61876772-T-C

Variant names:

• chr10-61876772-T-C
• rs2675609
• ENST00000717536.1:n.301+17360A>G

Variant summary

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

The ENST00000717536.1(LINC02625):​n.301+17360A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.608 in 152,056 control chromosomes in the GnomAD database, including 28,278 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 0.61 (28278 hom., cov: 32)
• Consequence: LINC02625 ENST00000717536.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.545
• Publications: 10 publications found

Genes affected

LINC02625 (HGNC:54104): (long intergenic non-protein coding RNA 2625)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.648 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000717536.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02625	ENST00000717536.1		n.301+17360A>G		intron	N/A
	LINC02625	ENST00000717537.1		n.426-13211A>G		intron	N/A
	LINC02625	ENST00000717538.1		n.215-13211A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.608 AC: 92313 AN: 151938 Hom.: 28256 Cov.: 32

Gnomad AFR AF: 0.655

Gnomad AMI AF: 0.418

Gnomad AMR AF: 0.464

Gnomad ASJ AF: 0.609

Gnomad EAS AF: 0.477

Gnomad SAS AF: 0.574

Gnomad FIN AF: 0.610

Gnomad MID AF: 0.586

Gnomad NFE AF: 0.626

Gnomad OTH AF: 0.607

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

GnomAD4 genome AF: 0.608 AC: 92375 AN: 152056 Hom.: 28278 Cov.: 32 AF XY: 0.602 AC XY: 44741 AN XY: 74332

African (AFR) AF: 0.655 AC: 27146 AN: 41458

American (AMR) AF: 0.463 AC: 7068 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.609 AC: 2111 AN: 3468

East Asian (EAS) AF: 0.477 AC: 2466 AN: 5174

South Asian (SAS) AF: 0.573 AC: 2763 AN: 4818

European-Finnish (FIN) AF: 0.610 AC: 6443 AN: 10562

Middle Eastern (MID) AF: 0.579 AC: 169 AN: 292

European-Non Finnish (NFE) AF: 0.626 AC: 42545 AN: 67988

Other (OTH) AF: 0.607 AC: 1283 AN: 2114

Alfa AF: 0.611 Hom.: 52459

Bravo AF: 0.593

Asia WGS AF: 0.594 AC: 2064 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	8.0
DANN	Benign	0.63
PhyloP100		0.55

Splicing

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

Other links and lift over

dbSNP: rs2675609; hg19: chr10-63636531;