chr4-138514635-A-G

Variant names:

• chr4-138514635-A-G
• rs10519469
• ENST00000653577.1:n.486-6921A>G

Variant summary

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

The ENST00000653577.1(LINC00499):​n.486-6921A>G variant causes a intron 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 ENST00000653577.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.491
• Publications: 3 publications found

Genes affected

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

ENSG00000297834 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000653577.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00499	ENST00000653577.1		n.486-6921A>G		intron	N/A
	LINC00499	ENST00000655654.1		n.597-6921A>G		intron	N/A
	LINC00499	ENST00000656561.1		n.468-6924A>G		intron	N/A

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

African (AFR) AF: 0.0487 AC: 2023 AN: 41572

American (AMR) AF: 0.0934 AC: 1427 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0524 AC: 182 AN: 3472

East Asian (EAS) AF: 0.0583 AC: 302 AN: 5178

South Asian (SAS) AF: 0.175 AC: 842 AN: 4820

European-Finnish (FIN) AF: 0.130 AC: 1381 AN: 10604

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

European-Non Finnish (NFE) AF: 0.0918 AC: 6240 AN: 68010

Other (OTH) AF: 0.0775 AC: 164 AN: 2116

Alfa AF: 0.0841 Hom.: 207

Bravo AF: 0.0767

Asia WGS AF: 0.121 AC: 421 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.65
DANN	Benign	0.60
PhyloP100		-0.49

Splicing

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

Other links and lift over

dbSNP: rs10519469; hg19: chr4-139435789;