chr4-138354902-G-A

Variant names:

• chr4-138354902-G-A
• rs10440463
• ENST00000507145.1:n.137-6394G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000507145.1(LINC00499):​n.137-6394G>A variant causes a intron 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 ENST00000507145.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.137
• 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=-0.95).
• 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 rank	MANE	Protein	UniProt
LINC00499	NR_051987.1	n.138-6394G>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00499	ENST00000507145.1	n.137-6394G>A		intron_variant	Intron 1 of 2	4
LINC00499	ENST00000510736.1	n.485+5052G>A		intron_variant	Intron 3 of 3	5
LINC00499	ENST00000653577.1	n.485+5052G>A		intron_variant	Intron 4 of 5

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

African (AFR) AF: 0.223 AC: 9238 AN: 41494

American (AMR) AF: 0.169 AC: 2577 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.190 AC: 659 AN: 3472

East Asian (EAS) AF: 0.229 AC: 1183 AN: 5156

South Asian (SAS) AF: 0.126 AC: 606 AN: 4818

European-Finnish (FIN) AF: 0.285 AC: 3010 AN: 10562

Middle Eastern (MID) AF: 0.238 AC: 70 AN: 294

European-Non Finnish (NFE) AF: 0.229 AC: 15547 AN: 67960

Other (OTH) AF: 0.208 AC: 439 AN: 2114

Alfa AF: 0.225 Hom.: 501

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
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs10440463; hg19: chr4-139276056;