rs10053502

Variant names:

• chr5-39979070-C-T
• rs10053502
• ENST00000638070.1:n.203+53812C>T

Variant summary

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

The ENST00000638070.1(LINC00603):​n.203+53812C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0681 in 152,200 control chromosomes in the GnomAD database, including 543 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 0.068 (543 hom., cov: 33)
• Consequence: LINC00603 ENST00000638070.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0310
• Publications: 8 publications found

Genes affected

LINC00603 (HGNC:43918): (long intergenic non-protein coding RNA 603)

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 = 0.143 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00603	ENST00000638070.1	n.203+53812C>T		intron_variant	Intron 2 of 2	5

Frequencies

GnomAD3 genomes AF: 0.0679 AC: 10329 AN: 152082 Hom.: 531 Cov.: 33

Gnomad AFR AF: 0.146

Gnomad AMI AF: 0.0132

Gnomad AMR AF: 0.0309

Gnomad ASJ AF: 0.0378

Gnomad EAS AF: 0.0571

Gnomad SAS AF: 0.0698

Gnomad FIN AF: 0.0274

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0382

Gnomad OTH AF: 0.0611

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

GnomAD4 genome AF: 0.0681 AC: 10367 AN: 152200 Hom.: 543 Cov.: 33 AF XY: 0.0661 AC XY: 4918 AN XY: 74424

African (AFR) AF: 0.147 AC: 6082 AN: 41512

American (AMR) AF: 0.0309 AC: 472 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0378 AC: 131 AN: 3470

East Asian (EAS) AF: 0.0565 AC: 293 AN: 5188

South Asian (SAS) AF: 0.0703 AC: 339 AN: 4824

European-Finnish (FIN) AF: 0.0274 AC: 290 AN: 10602

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.0383 AC: 2601 AN: 67996

Other (OTH) AF: 0.0605 AC: 128 AN: 2116

Alfa AF: 0.0587 Hom.: 725

Bravo AF: 0.0722

Asia WGS AF: 0.0580 AC: 201 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.9
DANN	Benign	0.79
PhyloP100		-0.031

Splicing

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

Other links and lift over

dbSNP: rs10053502; hg19: chr5-39979172;