rs4948288

Variant names:

• chr10-61824775-G-A
• rs4948288
• ENST00000717519.1:n.215-30310C>T

Variant summary

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

The ENST00000717519.1(LINC02625):​n.215-30310C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.339 in 151,756 control chromosomes in the GnomAD database, including 9,066 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 0.34 (9066 hom., cov: 32)
• Consequence: LINC02625 ENST00000717519.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.50
• Publications: 5 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 (NFE) allele frequency at 95% confidence interval = 0.399 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02625	XR_001747458.2	n.185-30310C>T		intron_variant	Intron 2 of 5
LINC02625	XR_001747460.2	n.304-30310C>T		intron_variant	Intron 2 of 5
LINC02625	XR_001747461.2	n.188-30310C>T		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02625	ENST00000717519.1	n.215-30310C>T		intron_variant	Intron 2 of 3
LINC02625	ENST00000717533.1	n.223+5887C>T		intron_variant	Intron 1 of 3
LINC02625	ENST00000717534.1	n.218-30310C>T		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.339 AC: 51389 AN: 151638 Hom.: 9065 Cov.: 32

Gnomad AFR AF: 0.271

Gnomad AMI AF: 0.170

Gnomad AMR AF: 0.283

Gnomad ASJ AF: 0.421

Gnomad EAS AF: 0.356

Gnomad SAS AF: 0.375

Gnomad FIN AF: 0.240

Gnomad MID AF: 0.325

Gnomad NFE AF: 0.402

Gnomad OTH AF: 0.335

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

GnomAD4 genome AF: 0.339 AC: 51418 AN: 151756 Hom.: 9066 Cov.: 32 AF XY: 0.331 AC XY: 24523 AN XY: 74126

African (AFR) AF: 0.271 AC: 11198 AN: 41332

American (AMR) AF: 0.283 AC: 4321 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.421 AC: 1460 AN: 3466

East Asian (EAS) AF: 0.355 AC: 1833 AN: 5160

South Asian (SAS) AF: 0.375 AC: 1799 AN: 4802

European-Finnish (FIN) AF: 0.240 AC: 2516 AN: 10494

Middle Eastern (MID) AF: 0.315 AC: 92 AN: 292

European-Non Finnish (NFE) AF: 0.403 AC: 27334 AN: 67908

Other (OTH) AF: 0.336 AC: 710 AN: 2110

Alfa AF: 0.385 Hom.: 6172

Bravo AF: 0.335

Asia WGS AF: 0.378 AC: 1314 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	7.2
DANN	Benign	0.75
PhyloP100		1.5

Splicing

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

Other links and lift over

dbSNP: rs4948288; hg19: chr10-63584533;