5-99544595-A-G

Variant names:

• chr5-99544595-A-G
• rs17167021
• ENST00000510302.2:n.728-4818A>G

Variant summary

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

The ENST00000510302.2(LINC02113):​n.728-4818A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0323 in 152,044 control chromosomes in the GnomAD database, including 114 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 0.032 (114 hom., cov: 32)
• Consequence: LINC02113 ENST00000510302.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.111
• Publications: 4 publications found

Genes affected

LINC02113 (HGNC:52967): (long intergenic non-protein coding RNA 2113)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0617 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02113	NR_110562.1	n.682-4818A>G		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02113	ENST00000510302.2	n.728-4818A>G		intron_variant	Intron 4 of 5	3
LINC02113	ENST00000844080.1	n.552-33128A>G		intron_variant	Intron 2 of 2
LINC02113	ENST00000844081.1	n.718-4818A>G		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.0321 AC: 4880 AN: 151926 Hom.: 106 Cov.: 32

Gnomad AFR AF: 0.0545

Gnomad AMI AF: 0.0121

Gnomad AMR AF: 0.0286

Gnomad ASJ AF: 0.0430

Gnomad EAS AF: 0.0585

Gnomad SAS AF: 0.0674

Gnomad FIN AF: 0.00443

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0184

Gnomad OTH AF: 0.0436

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

GnomAD4 genome AF: 0.0323 AC: 4915 AN: 152044 Hom.: 114 Cov.: 32 AF XY: 0.0327 AC XY: 2433 AN XY: 74352

African (AFR) AF: 0.0551 AC: 2290 AN: 41526

American (AMR) AF: 0.0285 AC: 434 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.0430 AC: 149 AN: 3464

East Asian (EAS) AF: 0.0585 AC: 302 AN: 5164

South Asian (SAS) AF: 0.0677 AC: 327 AN: 4830

European-Finnish (FIN) AF: 0.00443 AC: 47 AN: 10618

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.0184 AC: 1247 AN: 67886

Other (OTH) AF: 0.0441 AC: 93 AN: 2110

Alfa AF: 0.0228 Hom.: 77

Bravo AF: 0.0341

Asia WGS AF: 0.0510 AC: 176 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.3
DANN	Benign	0.40
PhyloP100		0.11

Splicing

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

Other links and lift over

dbSNP: rs17167021; hg19: chr5-98880299;