5-18714099-C-T

Variant names:

• chr5-18714099-C-T
• rs748418
• ENST00000512978.1:n.177-9605G>A

Variant summary

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

The ENST00000512978.1(LINC02100):​n.177-9605G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.152 in 151,786 control chromosomes in the GnomAD database, including 2,233 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 (2233 hom., cov: 32)
• Consequence: LINC02100 ENST00000512978.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.328
• Publications: 4 publications found

Genes affected

LINC02100 (HGNC:52955): (long intergenic non-protein coding RNA 2100)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.264 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02100	ENST00000512978.1	n.177-9605G>A		intron_variant	Intron 1 of 1	3

Frequencies

GnomAD3 genomes AF: 0.152 AC: 23102 AN: 151666 Hom.: 2232 Cov.: 32

Gnomad AFR AF: 0.0516

Gnomad AMI AF: 0.206

Gnomad AMR AF: 0.256

Gnomad ASJ AF: 0.154

Gnomad EAS AF: 0.121

Gnomad SAS AF: 0.276

Gnomad FIN AF: 0.154

Gnomad MID AF: 0.236

Gnomad NFE AF: 0.182

Gnomad OTH AF: 0.176

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

GnomAD4 genome AF: 0.152 AC: 23100 AN: 151786 Hom.: 2233 Cov.: 32 AF XY: 0.155 AC XY: 11495 AN XY: 74202

African (AFR) AF: 0.0516 AC: 2139 AN: 41480

American (AMR) AF: 0.256 AC: 3894 AN: 15184

Ashkenazi Jewish (ASJ) AF: 0.154 AC: 533 AN: 3470

East Asian (EAS) AF: 0.120 AC: 621 AN: 5162

South Asian (SAS) AF: 0.276 AC: 1332 AN: 4828

European-Finnish (FIN) AF: 0.154 AC: 1629 AN: 10592

Middle Eastern (MID) AF: 0.224 AC: 66 AN: 294

European-Non Finnish (NFE) AF: 0.182 AC: 12334 AN: 67758

Other (OTH) AF: 0.173 AC: 364 AN: 2106

Alfa AF: 0.179 Hom.: 1424

Bravo AF: 0.153

Asia WGS AF: 0.190 AC: 662 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	3.8
DANN	Benign	0.85
PhyloP100		0.33

Splicing

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

Other links and lift over

dbSNP: rs748418; hg19: chr5-18714208;