rs1451508955

Variant names:

• chr1-166850259-T-C
• rs1451508955
• NM_017542.5:c.1680T>C

Your query was ambiguous. Multiple possible variants found:

• chr1-166850259-T-C
• chr1-166850259-T-G

Variant summary

Our verdict is Likely benign. The variant received -3 ACMG points: 2P and 5B. PM2 BP4_Strong BP7

The NM_017542.5(POGK):​c.1680T>C​(p.Ser560Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000024 in 1,415,302 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: 33)
  • Exomes 𝑓: 0.000024 (0 hom.)
• Consequence: POGK NM_017542.5 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.22
• Publications: 0 publications found

Genes affected

POGK (HGNC:18800): (pogo transposable element derived with KRAB domain) The exact function of the protein encoded by this gene is not known. However, this gene product contains a KRAB domain (which is involved in protein-protein interactions) at the N-terminus, and a transposase domain at the C-terminus, suggesting that it may belong to the family of DNA-mediated transposons in human. [provided by RefSeq, Jul 2008]

ACMG classification

Our verdict: Likely_benign. The variant received -3 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BP7: Synonymous conserved (PhyloP=-2.22 with no splicing effect.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
POGK	NM_017542.5	c.1680T>C	p.Ser560Ser	synonymous_variant	Exon 5 of 6	ENST00000367876.9	NP_060012.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
POGK	ENST00000367876.9	c.1680T>C	p.Ser560Ser	synonymous_variant	Exon 5 of 6	1	NM_017542.5	ENSP00000356850.4
POGK	ENST00000367875.1	c.1680T>C	p.Ser560Ser	synonymous_variant	Exon 5 of 5	5		ENSP00000356849.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD2 exomes AF: 0.00000557 AC: 1 AN: 179552 AF XY: 0.0000105

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.0000138

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.0000240 AC: 34 AN: 1415302 Hom.: 0 Cov.: 32 AF XY: 0.0000200 AC XY: 14 AN XY: 699482

African (AFR) AF: 0.0000309 AC: 1 AN: 32332

American (AMR) AF: 0.00 AC: 0 AN: 37564

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 25390

East Asian (EAS) AF: 0.00 AC: 0 AN: 37078

South Asian (SAS) AF: 0.00 AC: 0 AN: 80874

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 50606

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5716

European-Non Finnish (NFE) AF: 0.0000285 AC: 31 AN: 1086968

Other (OTH) AF: 0.0000340 AC: 2 AN: 58774

GnomAD4 genome Cov.: 33

Alfa AF: 0.00 Hom.: 0

Bravo AF: 0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.3
DANN	Benign	0.34
PhyloP100		-2.2
Mutation Taster		=100/0	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs1451508955; hg19: chr1-166819496;