5-39950164-G-T

Variant names:

• chr5-39950164-G-T
• rs495237
• ENST00000638070.1:n.203+24906G>T

Variant summary

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

The ENST00000638070.1(LINC00603):​n.203+24906G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.259 in 151,556 control chromosomes in the GnomAD database, including 5,125 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 0.26 (5125 hom., cov: 31)
• Consequence: LINC00603 ENST00000638070.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.54

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.349 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+24906G>T		intron_variant	Intron 2 of 2	5

Frequencies

GnomAD3 genomes AF: 0.259 AC: 39262 AN: 151442 Hom.: 5113 Cov.: 31

Gnomad AFR AF: 0.270

Gnomad AMI AF: 0.333

Gnomad AMR AF: 0.211

Gnomad ASJ AF: 0.343

Gnomad EAS AF: 0.262

Gnomad SAS AF: 0.363

Gnomad FIN AF: 0.197

Gnomad MID AF: 0.350

Gnomad NFE AF: 0.259

Gnomad OTH AF: 0.273

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

GnomAD4 genome AF: 0.259 AC: 39308 AN: 151556 Hom.: 5125 Cov.: 31 AF XY: 0.258 AC XY: 19099 AN XY: 74030

Gnomad4 AFR AF: 0.271

Gnomad4 AMR AF: 0.211

Gnomad4 ASJ AF: 0.343

Gnomad4 EAS AF: 0.262

Gnomad4 SAS AF: 0.364

Gnomad4 FIN AF: 0.197

Gnomad4 NFE AF: 0.259

Gnomad4 OTH AF: 0.270

Alfa AF: 0.212 Hom.: 982

Bravo AF: 0.259

Asia WGS AF: 0.333 AC: 1154 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.057
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs495237; hg19: chr5-39950266;