chr5-18712250-T-A

Variant names:

• chr5-18712250-T-A
• rs11959018
• ENST00000512978.1:n.177-7756A>T

Variant summary

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

The ENST00000512978.1(LINC02100):​n.177-7756A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.227 in 152,082 control chromosomes in the GnomAD database, including 4,233 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 0.23 (4233 hom., cov: 32)
• Consequence: LINC02100 ENST00000512978.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.243
• Publications: 1 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=-0.99).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.284 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.177-7756A>T		intron_variant	Intron 1 of 1	3

Frequencies

GnomAD3 genomes AF: 0.227 AC: 34552 AN: 151966 Hom.: 4227 Cov.: 32

Gnomad AFR AF: 0.280

Gnomad AMI AF: 0.206

Gnomad AMR AF: 0.291

Gnomad ASJ AF: 0.173

Gnomad EAS AF: 0.174

Gnomad SAS AF: 0.295

Gnomad FIN AF: 0.157

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.194

Gnomad OTH AF: 0.229

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

GnomAD4 genome AF: 0.227 AC: 34576 AN: 152082 Hom.: 4233 Cov.: 32 AF XY: 0.228 AC XY: 16927 AN XY: 74354

African (AFR) AF: 0.280 AC: 11608 AN: 41514

American (AMR) AF: 0.292 AC: 4445 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.173 AC: 602 AN: 3472

East Asian (EAS) AF: 0.173 AC: 895 AN: 5174

South Asian (SAS) AF: 0.295 AC: 1426 AN: 4828

European-Finnish (FIN) AF: 0.157 AC: 1669 AN: 10600

Middle Eastern (MID) AF: 0.269 AC: 79 AN: 294

European-Non Finnish (NFE) AF: 0.194 AC: 13186 AN: 67930

Other (OTH) AF: 0.226 AC: 478 AN: 2114

Alfa AF: 0.0870 Hom.: 116

Bravo AF: 0.239

Asia WGS AF: 0.256 AC: 892 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.5
DANN	Benign	0.56
PhyloP100		0.24

Splicing

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

Other links and lift over

dbSNP: rs11959018; hg19: chr5-18712359;