rs11736129

Variant names:

• chr4-138464472-C-G
• rs11736129
• ENST00000653577.1:n.486-57084C>G

Variant summary

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

The ENST00000653577.1(LINC00499):​n.486-57084C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.141 in 152,094 control chromosomes in the GnomAD database, including 2,068 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 0.14 (2068 hom., cov: 31)
• Consequence: LINC00499 ENST00000653577.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.358

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 (EAS) allele frequency at 95% confidence interval = 0.483 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
LINC00499	ENST00000653577.1	n.486-57084C>G		intron_variant	Intron 4 of 5
LINC00499	ENST00000655654.1	n.597-57084C>G		intron_variant	Intron 4 of 5
LINC00499	ENST00000656561.1	n.468-57087C>G		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.141 AC: 21414 AN: 151978 Hom.: 2072 Cov.: 31

Gnomad AFR AF: 0.122

Gnomad AMI AF: 0.0658

Gnomad AMR AF: 0.224

Gnomad ASJ AF: 0.0600

Gnomad EAS AF: 0.501

Gnomad SAS AF: 0.205

Gnomad FIN AF: 0.153

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.106

Gnomad OTH AF: 0.129

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

GnomAD4 genome AF: 0.141 AC: 21417 AN: 152094 Hom.: 2068 Cov.: 31 AF XY: 0.149 AC XY: 11064 AN XY: 74334

Gnomad4 AFR AF: 0.122

Gnomad4 AMR AF: 0.224

Gnomad4 ASJ AF: 0.0600

Gnomad4 EAS AF: 0.499

Gnomad4 SAS AF: 0.206

Gnomad4 FIN AF: 0.153

Gnomad4 NFE AF: 0.106

Gnomad4 OTH AF: 0.131

Alfa AF: 0.126 Hom.: 180

Bravo AF: 0.147

Asia WGS AF: 0.349 AC: 1212 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	1.0
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11736129; hg19: chr4-139385626;