rs11736129

Positions:

• chr4-138464472-C-G

Variant summary

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

The ENST00000663528.1(LINC00499):​n.453-57084C>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 0.141 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 ENST00000663528.1 intron, non_coding_transcript
• 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC00499	ENST00000663528.1	n.453-57084C>G		intron_variant, non_coding_transcript_variant

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;