rs1499111

Variant names:

• chr4-128551184-C-T
• rs1499111
• ENST00000816105.1:n.568-5806C>T

Variant summary

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

The ENST00000816105.1(LINC02615):​n.568-5806C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.255 in 152,048 control chromosomes in the GnomAD database, including 5,646 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 0.26 (5646 hom., cov: 32)
• Consequence: LINC02615 ENST00000816105.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.694
• Publications: 6 publications found

Genes affected

LINC02615 (HGNC:53402): (long intergenic non-protein coding RNA 2615)

ENSG00000273077 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.394 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101927259	NR_187927.1	n.1180+255G>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02615	ENST00000816105.1	n.568-5806C>T		intron_variant	Intron 5 of 5
ENSG00000273077	ENST00000816287.1	n.1182+255G>A		intron_variant	Intron 2 of 2
ENSG00000273077	ENST00000816288.1	n.1248+255G>A		intron_variant	Intron 3 of 3
ENSG00000273077	ENST00000816289.1	n.88-1929G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.255 AC: 38740 AN: 151930 Hom.: 5628 Cov.: 32

Gnomad AFR AF: 0.399

Gnomad AMI AF: 0.109

Gnomad AMR AF: 0.225

Gnomad ASJ AF: 0.203

Gnomad EAS AF: 0.0572

Gnomad SAS AF: 0.177

Gnomad FIN AF: 0.223

Gnomad MID AF: 0.271

Gnomad NFE AF: 0.204

Gnomad OTH AF: 0.259

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

GnomAD4 genome AF: 0.255 AC: 38801 AN: 152048 Hom.: 5646 Cov.: 32 AF XY: 0.254 AC XY: 18872 AN XY: 74340

African (AFR) AF: 0.399 AC: 16520 AN: 41412

American (AMR) AF: 0.226 AC: 3450 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.203 AC: 705 AN: 3472

East Asian (EAS) AF: 0.0569 AC: 295 AN: 5184

South Asian (SAS) AF: 0.177 AC: 851 AN: 4820

European-Finnish (FIN) AF: 0.223 AC: 2358 AN: 10580

Middle Eastern (MID) AF: 0.277 AC: 81 AN: 292

European-Non Finnish (NFE) AF: 0.204 AC: 13896 AN: 67976

Other (OTH) AF: 0.259 AC: 546 AN: 2110

Alfa AF: 0.217 Hom.: 2128

Bravo AF: 0.261

Asia WGS AF: 0.176 AC: 610 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.9
DANN	Benign	0.42
PhyloP100		-0.69

Splicing

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

Other links and lift over

dbSNP: rs1499111; hg19: chr4-129472339;