rs10440463

chr4-138354902-G-Achr4-138354902-G-C

Variant summary

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

The NR_051987.1(LINC00499):n.138-6394G>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 0.22 in 152,054 control chromosomes in the GnomAD database, including 3,890 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 0.22 (3890 hom., cov: 32)
• Consequence: LINC00499 NR_051987.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.137

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=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.226 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC00499	NR_051987.1	n.138-6394G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00499	ENST00000663528.1	n.452+5052G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.220 AC: 33476 AN: 151936 Hom.: 3889 Cov.: 32

Gnomad AFR AF: 0.223

Gnomad AMI AF: 0.176

Gnomad AMR AF: 0.169

Gnomad ASJ AF: 0.190

Gnomad EAS AF: 0.229

Gnomad SAS AF: 0.125

Gnomad FIN AF: 0.285

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.229

Gnomad OTH AF: 0.209

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

GnomAD4 genome AF: 0.220 AC: 33489 AN: 152054 Hom.: 3890 Cov.: 32 AF XY: 0.218 AC XY: 16224 AN XY: 74312

Gnomad4 AFR AF: 0.223

Gnomad4 AMR AF: 0.169

Gnomad4 ASJ AF: 0.190

Gnomad4 EAS AF: 0.229

Gnomad4 SAS AF: 0.126

Gnomad4 FIN AF: 0.285

Gnomad4 NFE AF: 0.229

Gnomad4 OTH AF: 0.208

Alfa AF: 0.225 Hom.: 478

Bravo AF: 0.214

Asia WGS AF: 0.165 AC: 572 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	2.8
Dann	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10440463; hg19: chr4-139276056;