4-138415015-C-T

Position:

• chr4-138415015-C-T

Variant summary

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

The NR_051987.1(LINC00499):​n.245-9033C>T 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 0.861 in 152,268 control chromosomes in the GnomAD database, including 57,019 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 0.86 (57019 hom., cov: 34)
• Consequence: LINC00499 NR_051987.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.593

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=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.893 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC00499	NR_051987.1	n.245-9033C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00499	ENST00000663528.1	n.452+65165C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.861 AC: 131017 AN: 152150 Hom.: 56970 Cov.: 34

Gnomad AFR AF: 0.900

Gnomad AMI AF: 0.882

Gnomad AMR AF: 0.770

Gnomad ASJ AF: 0.944

Gnomad EAS AF: 0.525

Gnomad SAS AF: 0.787

Gnomad FIN AF: 0.858

Gnomad MID AF: 0.965

Gnomad NFE AF: 0.884

Gnomad OTH AF: 0.871

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

GnomAD4 genome AF: 0.861 AC: 131131 AN: 152268 Hom.: 57019 Cov.: 34 AF XY: 0.854 AC XY: 63574 AN XY: 74444

Gnomad4 AFR AF: 0.900

Gnomad4 AMR AF: 0.770

Gnomad4 ASJ AF: 0.944

Gnomad4 EAS AF: 0.526

Gnomad4 SAS AF: 0.786

Gnomad4 FIN AF: 0.858

Gnomad4 NFE AF: 0.884

Gnomad4 OTH AF: 0.865

Alfa AF: 0.874 Hom.: 7841

Bravo AF: 0.855

Asia WGS AF: 0.680 AC: 2368 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.17
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1365372; hg19: chr4-139336169;