chr4-38454752-G-C

Variant names:

• chr4-38454752-G-C
• rs10517483
• ENST00000512517.1:n.185-831C>G

Variant summary

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

The ENST00000512517.1(LINC01258):​n.185-831C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0484 in 152,234 control chromosomes in the GnomAD database, including 702 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 0.048 (702 hom., cov: 32)
• Consequence: LINC01258 ENST00000512517.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.987
• Publications: 1 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=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.378 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01258	NR_110951.1	n.185-831C>G		intron_variant	Intron 2 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01258	ENST00000512517.1	n.185-831C>G		intron_variant	Intron 2 of 7	2
LINC01258	ENST00000653888.1	n.50-831C>G		intron_variant	Intron 1 of 4
LINC01258	ENST00000669996.1	n.87-831C>G		intron_variant	Intron 1 of 2
LINC01258	ENST00000774213.1	n.67-831C>G		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.0484 AC: 7368 AN: 152116 Hom.: 704 Cov.: 32

Gnomad AFR AF: 0.00990

Gnomad AMI AF: 0.0154

Gnomad AMR AF: 0.169

Gnomad ASJ AF: 0.0176

Gnomad EAS AF: 0.392

Gnomad SAS AF: 0.0350

Gnomad FIN AF: 0.0298

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.0246

Gnomad OTH AF: 0.0541

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

GnomAD4 genome AF: 0.0484 AC: 7369 AN: 152234 Hom.: 702 Cov.: 32 AF XY: 0.0526 AC XY: 3915 AN XY: 74438

African (AFR) AF: 0.00987 AC: 410 AN: 41552

American (AMR) AF: 0.169 AC: 2583 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0176 AC: 61 AN: 3468

East Asian (EAS) AF: 0.392 AC: 2024 AN: 5164

South Asian (SAS) AF: 0.0353 AC: 170 AN: 4822

European-Finnish (FIN) AF: 0.0298 AC: 316 AN: 10608

Middle Eastern (MID) AF: 0.00340 AC: 1 AN: 294

European-Non Finnish (NFE) AF: 0.0246 AC: 1676 AN: 68012

Other (OTH) AF: 0.0540 AC: 114 AN: 2112

Alfa AF: 0.0355 Hom.: 33

Bravo AF: 0.0592

Asia WGS AF: 0.165 AC: 573 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	8.1
DANN	Benign	0.48
PhyloP100		0.99
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs10517483; hg19: chr4-38456373;