rs1517853

Variant names:

• chr2-104681545-A-C
• rs1517853
• ENST00000669335.1:n.4095-24542T>G

Your query was ambiguous. Multiple possible variants found:

• chr2-104681545-A-C
• chr2-104681545-A-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000669335.1(PANTR1):​n.4095-24542T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
• Consequence: PANTR1 ENST00000669335.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.53
• Publications: 1 publications found

Genes affected

PANTR1 (HGNC:49513): (POU3F3 adjacent non-coding transcript 1) Predicted to act upstream of or within regulation of gene expression. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000230690 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105373526	NR_188087.1	n.1124-3175A>C		intron_variant	Intron 6 of 6
LOC105373526	NR_188088.1	n.1168+1065A>C		intron_variant	Intron 7 of 8
LOC105373526	NR_188089.1	n.988+1065A>C		intron_variant	Intron 7 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PANTR1	ENST00000669335.1	n.4095-24542T>G		intron_variant	Intron 1 of 1
PANTR1	ENST00000715830.1	n.1419-24542T>G		intron_variant	Intron 4 of 4
PANTR1	ENST00000733170.1	n.1715-24542T>G		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	5.1
DANN	Benign	0.69
PhyloP100		1.5

Splicing

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

Other links and lift over

dbSNP: rs1517853; hg19: chr2-105298003;