rs17076203

Variant names:

• chr6-114544616-A-G
• rs17076203
• ENST00000435802.3:n.85+628T>C

Variant summary

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

The ENST00000435802.3(LNCPOIR):​n.85+628T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.117 in 152,238 control chromosomes in the GnomAD database, including 1,040 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 0.12 (1040 hom., cov: 32)
• Consequence: LNCPOIR ENST00000435802.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0880
• Publications: 2 publications found

Genes affected

LNCPOIR (HGNC:54521): (lncRNA periodontal mesenchymal stem cell osteogenesis related)

HDAC2-AS2 (HGNC:43590): (HDAC2 and HS3ST5 antisense RNA 2)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.122 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LNCPOIR	NR_183487.1	n.77+628T>C		intron_variant	Intron 1 of 3
LNCPOIR	NR_183488.1	n.77+628T>C		intron_variant	Intron 1 of 3
LNCPOIR	NR_183489.1	n.77+628T>C		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LNCPOIR	ENST00000435802.3	n.85+628T>C		intron_variant	Intron 1 of 3	3
LNCPOIR	ENST00000652989.2	n.108+628T>C		intron_variant	Intron 1 of 2
HDAC2-AS2	ENST00000826283.1	n.668-3551A>G		intron_variant	Intron 5 of 5

Frequencies

GnomAD3 genomes AF: 0.117 AC: 17823 AN: 152120 Hom.: 1033 Cov.: 32

Gnomad AFR AF: 0.109

Gnomad AMI AF: 0.118

Gnomad AMR AF: 0.0869

Gnomad ASJ AF: 0.145

Gnomad EAS AF: 0.0896

Gnomad SAS AF: 0.114

Gnomad FIN AF: 0.153

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.124

Gnomad OTH AF: 0.111

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

GnomAD4 genome AF: 0.117 AC: 17854 AN: 152238 Hom.: 1040 Cov.: 32 AF XY: 0.119 AC XY: 8833 AN XY: 74418

African (AFR) AF: 0.110 AC: 4563 AN: 41552

American (AMR) AF: 0.0868 AC: 1328 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.145 AC: 504 AN: 3470

East Asian (EAS) AF: 0.0896 AC: 464 AN: 5178

South Asian (SAS) AF: 0.116 AC: 558 AN: 4830

European-Finnish (FIN) AF: 0.153 AC: 1623 AN: 10584

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.124 AC: 8455 AN: 68008

Other (OTH) AF: 0.109 AC: 231 AN: 2112

Alfa AF: 0.119 Hom.: 1817

Bravo AF: 0.111

Asia WGS AF: 0.0950 AC: 329 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	7.2
DANN	Benign	0.85
PhyloP100		0.088

Splicing

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

Other links and lift over

dbSNP: rs17076203; hg19: chr6-114865780;