rs4615179

Variant names:

• chr4-38463850-C-T
• rs4615179
• ENST00000512517.1:n.185-9929G>A

Variant summary

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

The ENST00000512517.1(LINC01258):​n.185-9929G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.148 in 151,952 control chromosomes in the GnomAD database, including 1,948 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 0.15 (1948 hom., cov: 32)
• Consequence: LINC01258 ENST00000512517.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -5.07
• Publications: 3 publications found

Genes affected

LINC01258 (HGNC:49898): (long intergenic non-protein coding RNA 1258)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.215 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01258	NR_110951.1	n.185-9929G>A		intron_variant	Intron 2 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01258	ENST00000512517.1	n.185-9929G>A		intron_variant	Intron 2 of 7	2
LINC01258	ENST00000653888.1	n.50-9929G>A		intron_variant	Intron 1 of 4
LINC01258	ENST00000669996.1	n.87-9929G>A		intron_variant	Intron 1 of 2
LINC01258	ENST00000774213.1	n.67-9929G>A		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.148 AC: 22453 AN: 151834 Hom.: 1943 Cov.: 32

Gnomad AFR AF: 0.219

Gnomad AMI AF: 0.0691

Gnomad AMR AF: 0.106

Gnomad ASJ AF: 0.0706

Gnomad EAS AF: 0.0642

Gnomad SAS AF: 0.133

Gnomad FIN AF: 0.220

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.115

Gnomad OTH AF: 0.143

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

GnomAD4 genome AF: 0.148 AC: 22494 AN: 151952 Hom.: 1948 Cov.: 32 AF XY: 0.152 AC XY: 11287 AN XY: 74260

African (AFR) AF: 0.219 AC: 9069 AN: 41436

American (AMR) AF: 0.106 AC: 1620 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.0706 AC: 245 AN: 3468

East Asian (EAS) AF: 0.0644 AC: 332 AN: 5158

South Asian (SAS) AF: 0.133 AC: 642 AN: 4810

European-Finnish (FIN) AF: 0.220 AC: 2319 AN: 10534

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.115 AC: 7850 AN: 67974

Other (OTH) AF: 0.145 AC: 305 AN: 2102

Alfa AF: 0.127 Hom.: 2729

Bravo AF: 0.140

Asia WGS AF: 0.120 AC: 420 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.011
DANN	Benign	0.62
PhyloP100		-5.1

Splicing

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

Other links and lift over

dbSNP: rs4615179; hg19: chr4-38465471;