4-138632962-G-C

Variant names:

• chr4-138632962-G-C
• rs13120622
• ENST00000663528.1:n.677+3309G>C

Variant summary

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

The ENST00000663528.1(LINC00499):​n.677+3309G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.579 in 151,926 control chromosomes in the GnomAD database, including 25,830 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 0.58 (25830 hom., cov: 32)
• Consequence: LINC00499 ENST00000663528.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.423

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=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.619 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	ENST00000663528.1	n.677+3309G>C		intron_variant	Intron 5 of 6
LINC00499	ENST00000667838.1	n.767+3309G>C		intron_variant	Intron 6 of 6

Frequencies

GnomAD3 genomes AF: 0.579 AC: 87948 AN: 151808 Hom.: 25817 Cov.: 32

Gnomad AFR AF: 0.591

Gnomad AMI AF: 0.618

Gnomad AMR AF: 0.469

Gnomad ASJ AF: 0.593

Gnomad EAS AF: 0.435

Gnomad SAS AF: 0.517

Gnomad FIN AF: 0.497

Gnomad MID AF: 0.639

Gnomad NFE AF: 0.624

Gnomad OTH AF: 0.586

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

GnomAD4 genome AF: 0.579 AC: 88006 AN: 151926 Hom.: 25830 Cov.: 32 AF XY: 0.570 AC XY: 42345 AN XY: 74234

Gnomad4 AFR AF: 0.591

Gnomad4 AMR AF: 0.468

Gnomad4 ASJ AF: 0.593

Gnomad4 EAS AF: 0.436

Gnomad4 SAS AF: 0.517

Gnomad4 FIN AF: 0.497

Gnomad4 NFE AF: 0.624

Gnomad4 OTH AF: 0.583

Alfa AF: 0.601 Hom.: 3438

Bravo AF: 0.574

Asia WGS AF: 0.447 AC: 1554 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	5.8
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13120622; hg19: chr4-139554116;