rs12659118

Positions:

• chr5-150945060-T-C
• chr5-150945060-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_026867.1(ZNF300P1):​n.280-1188A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0962 in 152,224 control chromosomes in the GnomAD database, including 1,060 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 0.096 (1060 hom., cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: ZNF300P1 NR_026867.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.81

Genes affected

ZNF300P1 (HGNC:27032): (zinc finger protein 300 pseudogene 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.67).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.397 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZNF300P1	NR_026867.1	n.280-1188A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZNF300P1	ENST00000356555.6	n.13-1188A>G		intron_variant, non_coding_transcript_variant
ZNF300P1	ENST00000685103.1	n.294-1188A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0963 AC: 14646 AN: 152106 Hom.: 1060 Cov.: 32

Gnomad AFR AF: 0.0587

Gnomad AMI AF: 0.0296

Gnomad AMR AF: 0.109

Gnomad ASJ AF: 0.178

Gnomad EAS AF: 0.411

Gnomad SAS AF: 0.119

Gnomad FIN AF: 0.0999

Gnomad MID AF: 0.197

Gnomad NFE AF: 0.0854

Gnomad OTH AF: 0.131

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 2 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 2

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.0962 AC: 14639 AN: 152224 Hom.: 1060 Cov.: 32 AF XY: 0.0993 AC XY: 7388 AN XY: 74418

Gnomad4 AFR AF: 0.0586

Gnomad4 AMR AF: 0.109

Gnomad4 ASJ AF: 0.178

Gnomad4 EAS AF: 0.412

Gnomad4 SAS AF: 0.118

Gnomad4 FIN AF: 0.0999

Gnomad4 NFE AF: 0.0854

Gnomad4 OTH AF: 0.130

Alfa AF: 0.0884 Hom.: 323

Bravo AF: 0.0987

Asia WGS AF: 0.221 AC: 769 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	0.16
DANN	Benign	0.93

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12659118; hg19: chr5-150324622;