ENST00000356555.6:n.13-1188A>G

Variant names:

• chr5-150945060-T-C
• rs12659118
• ENST00000356555.6:n.13-1188A>G

Variant summary

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

The ENST00000356555.6(ZNF300P1):​n.13-1188A>G variant causes a intron 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 ENST00000356555.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.81
• Publications: 12 publications found

Genes affected

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

ENSG00000291115 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
ZNF300P1	NR_026867.1	n.280-1188A>G		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZNF300P1	ENST00000356555.6	n.13-1188A>G		intron_variant	Intron 1 of 4	6
ENSG00000291115	ENST00000685103.2	n.294-1188A>G		intron_variant	Intron 1 of 4
ENSG00000291115	ENST00000686020.2	n.213-1188A>G		intron_variant	Intron 1 of 4

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AF: 0.00 AC: 0 AN: 2

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

African (AFR) AF: 0.0586 AC: 2435 AN: 41550

American (AMR) AF: 0.109 AC: 1660 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.178 AC: 619 AN: 3470

East Asian (EAS) AF: 0.412 AC: 2130 AN: 5174

South Asian (SAS) AF: 0.118 AC: 569 AN: 4828

European-Finnish (FIN) AF: 0.0999 AC: 1058 AN: 10590

Middle Eastern (MID) AF: 0.202 AC: 59 AN: 292

European-Non Finnish (NFE) AF: 0.0854 AC: 5808 AN: 68002

Other (OTH) AF: 0.130 AC: 274 AN: 2112

Alfa AF: 0.0889 Hom.: 605

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
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs12659118; hg19: chr5-150324622;