4-138632962-G-C

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

Genes affected

LINC00499 (HGNC:43436): (long intergenic non-protein coding RNA 499)

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000663528.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00499	ENST00000663528.1		n.677+3309G>C		intron	N/A
	LINC00499	ENST00000667838.1		n.767+3309G>C		intron	N/A
	LINC00499	ENST00000815123.1		n.*189G>C		downstream_gene	N/A

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

African (AFR) AF: 0.591 AC: 24484 AN: 41426

American (AMR) AF: 0.468 AC: 7141 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.593 AC: 2057 AN: 3470

East Asian (EAS) AF: 0.436 AC: 2242 AN: 5148

South Asian (SAS) AF: 0.517 AC: 2486 AN: 4812

European-Finnish (FIN) AF: 0.497 AC: 5247 AN: 10558

Middle Eastern (MID) AF: 0.629 AC: 185 AN: 294

European-Non Finnish (NFE) AF: 0.624 AC: 42372 AN: 67954

Other (OTH) AF: 0.583 AC: 1228 AN: 2106

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	5.8
DANN	Benign	0.37
PhyloP100		0.42

Splicing

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

Other links and lift over

dbSNP: rs13120622; hg19: chr4-139554116;