rs6857347

Positions:

• chr4-138387591-G-A

Variant summary

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

The NR_051987.1(LINC00499):​n.244+26189G>A 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 0.453 in 151,762 control chromosomes in the GnomAD database, including 16,262 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 0.45 (16262 hom., cov: 31)
• Consequence: LINC00499 NR_051987.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0970

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=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.579 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC00499	NR_051987.1	n.244+26189G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC00499	ENST00000663528.1	n.452+37741G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.453 AC: 68737 AN: 151644 Hom.: 16254 Cov.: 31

Gnomad AFR AF: 0.384

Gnomad AMI AF: 0.367

Gnomad AMR AF: 0.338

Gnomad ASJ AF: 0.493

Gnomad EAS AF: 0.297

Gnomad SAS AF: 0.595

Gnomad FIN AF: 0.547

Gnomad MID AF: 0.545

Gnomad NFE AF: 0.507

Gnomad OTH AF: 0.469

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

GnomAD4 genome AF: 0.453 AC: 68777 AN: 151762 Hom.: 16262 Cov.: 31 AF XY: 0.452 AC XY: 33514 AN XY: 74148

Gnomad4 AFR AF: 0.383

Gnomad4 AMR AF: 0.338

Gnomad4 ASJ AF: 0.493

Gnomad4 EAS AF: 0.297

Gnomad4 SAS AF: 0.597

Gnomad4 FIN AF: 0.547

Gnomad4 NFE AF: 0.507

Gnomad4 OTH AF: 0.468

Alfa AF: 0.490 Hom.: 25097

Bravo AF: 0.427

Asia WGS AF: 0.449 AC: 1560 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	5.3
DANN	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6857347; hg19: chr4-139308745;