rs10519469

Positions:

• chr4-138514635-A-G

Variant summary

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

The ENST00000663528.1(LINC00499):​n.453-6921A>G 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 0.083 in 152,254 control chromosomes in the GnomAD database, including 585 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 0.083 (585 hom., cov: 32)
• Consequence: LINC00499 ENST00000663528.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.491

Genes affected

LINC00499 (HGNC:43436): (long intergenic non-protein coding RNA 499)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.165 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
LINC00499	ENST00000663528.1	n.453-6921A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0829 AC: 12612 AN: 152136 Hom.: 585 Cov.: 32

Gnomad AFR AF: 0.0487

Gnomad AMI AF: 0.0548

Gnomad AMR AF: 0.0931

Gnomad ASJ AF: 0.0524

Gnomad EAS AF: 0.0580

Gnomad SAS AF: 0.175

Gnomad FIN AF: 0.130

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0917

Gnomad OTH AF: 0.0740

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

GnomAD4 genome AF: 0.0830 AC: 12630 AN: 152254 Hom.: 585 Cov.: 32 AF XY: 0.0841 AC XY: 6257 AN XY: 74442

Gnomad4 AFR AF: 0.0487

Gnomad4 AMR AF: 0.0934

Gnomad4 ASJ AF: 0.0524

Gnomad4 EAS AF: 0.0583

Gnomad4 SAS AF: 0.175

Gnomad4 FIN AF: 0.130

Gnomad4 NFE AF: 0.0918

Gnomad4 OTH AF: 0.0775

Alfa AF: 0.0841 Hom.: 98

Bravo AF: 0.0767

Asia WGS AF: 0.121 AC: 421 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.65
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10519469; hg19: chr4-139435789;