rs4948288

Positions:

• chr10-61824775-G-A

Variant summary

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

The XR_001747461.2(LINC02625):​n.188-30310C>T 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 0.339 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 XR_001747461.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.50

Genes affected

LINC02625 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
LINC02625	XR_001747461.2	n.188-30310C>T		intron_variant, non_coding_transcript_variant
LINC02625	XR_001747458.2	n.185-30310C>T		intron_variant, non_coding_transcript_variant
LINC02625	XR_001747460.2	n.304-30310C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.271

Gnomad4 AMR AF: 0.283

Gnomad4 ASJ AF: 0.421

Gnomad4 EAS AF: 0.355

Gnomad4 SAS AF: 0.375

Gnomad4 FIN AF: 0.240

Gnomad4 NFE AF: 0.403

Gnomad4 OTH AF: 0.336

Alfa AF: 0.384 Hom.: 5565

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4948288; hg19: chr10-63584533;