5-39950164-G-T

Position:

• chr5-39950164-G-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, non coding transcript 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, non_coding_transcript
• 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC00603	ENST00000638070.1	n.203+24906G>T		intron_variant, non_coding_transcript_variant		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;