rs10004839

Variant names:

• chr4-137233658-C-T
• rs10004839
• ENST00000828076.1:n.592-641C>T

Variant summary

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

The ENST00000828076.1(LINC02510):​n.592-641C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0482 in 152,140 control chromosomes in the GnomAD database, including 285 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 0.048 (285 hom., cov: 32)
• Consequence: LINC02510 ENST00000828076.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0730
• Publications: 4 publications found

Genes affected

LINC02510 (HGNC:53499): (long intergenic non-protein coding RNA 2510)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0999 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000828076.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02510	ENST00000828076.1		n.592-641C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0482 AC: 7335 AN: 152022 Hom.: 285 Cov.: 32

Gnomad AFR AF: 0.103

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0307

Gnomad ASJ AF: 0.0130

Gnomad EAS AF: 0.0178

Gnomad SAS AF: 0.0769

Gnomad FIN AF: 0.0237

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0256

Gnomad OTH AF: 0.0502

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

GnomAD4 genome AF: 0.0482 AC: 7340 AN: 152140 Hom.: 285 Cov.: 32 AF XY: 0.0481 AC XY: 3580 AN XY: 74382

African (AFR) AF: 0.102 AC: 4250 AN: 41492

American (AMR) AF: 0.0306 AC: 468 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.0130 AC: 45 AN: 3468

East Asian (EAS) AF: 0.0176 AC: 91 AN: 5168

South Asian (SAS) AF: 0.0768 AC: 370 AN: 4820

European-Finnish (FIN) AF: 0.0237 AC: 251 AN: 10604

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.0256 AC: 1743 AN: 67992

Other (OTH) AF: 0.0521 AC: 110 AN: 2112

Alfa AF: 0.0336 Hom.: 329

Bravo AF: 0.0492

Asia WGS AF: 0.0420 AC: 146 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.69
DANN	Benign	0.59
PhyloP100		0.073

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10004839;

hg19: chr4-138154812;