chr4-153659136-A-G

Variant names:

• chr4-153659136-A-G
• rs17279573
• ENST00000602666.1:n.355+18119A>G

Variant summary

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

The ENST00000602666.1(ENSG00000290441):​n.355+18119A>G variant causes a intron change. The variant allele was found at a frequency of 0.149 in 1,598,682 control chromosomes in the GnomAD database, including 19,603 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 0.11 (1281 hom., cov: 33)
  • Exomes 𝑓: 0.15 (18322 hom.)
• Consequence: ENSG00000290441 ENST00000602666.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 5.95
• Publications: 5 publications found

Genes affected

ENSG00000290441 (HGNC:):

WDR45P1 (HGNC:52406): (WD repeat domain 45 pseudogene 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.57).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.291 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
WDR45P1		n.153659136A>G		intragenic_variant
LOC100419170	NR_134873.1	n.355+18119A>G		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000290441	ENST00000602666.1	n.355+18119A>G		intron_variant	Intron 2 of 2	1
WDR45P1	ENST00000502774.1	n.565A>G		non_coding_transcript_exon_variant	Exon 1 of 1	6
ENSG00000300572	ENST00000772789.1	n.53-164T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.114 AC: 17388 AN: 152040 Hom.: 1282 Cov.: 33

Gnomad AFR AF: 0.0277

Gnomad AMI AF: 0.0274

Gnomad AMR AF: 0.104

Gnomad ASJ AF: 0.0887

Gnomad EAS AF: 0.303

Gnomad SAS AF: 0.154

Gnomad FIN AF: 0.0925

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.158

Gnomad OTH AF: 0.128

GnomAD4 exome AF: 0.153 AC: 221323 AN: 1446524 Hom.: 18322 Cov.: 36 AF XY: 0.154 AC XY: 110958 AN XY: 720288

African (AFR) AF: 0.0218 AC: 725 AN: 33318

American (AMR) AF: 0.0928 AC: 4128 AN: 44466

Ashkenazi Jewish (ASJ) AF: 0.0817 AC: 2130 AN: 26056

East Asian (EAS) AF: 0.320 AC: 12670 AN: 39548

South Asian (SAS) AF: 0.157 AC: 13513 AN: 85848

European-Finnish (FIN) AF: 0.0987 AC: 5266 AN: 53352

Middle Eastern (MID) AF: 0.139 AC: 801 AN: 5748

European-Non Finnish (NFE) AF: 0.158 AC: 173344 AN: 1098304

Other (OTH) AF: 0.146 AC: 8746 AN: 59884

GnomAD4 genome AF: 0.114 AC: 17382 AN: 152158 Hom.: 1281 Cov.: 33 AF XY: 0.114 AC XY: 8455 AN XY: 74378

African (AFR) AF: 0.0276 AC: 1147 AN: 41544

American (AMR) AF: 0.104 AC: 1589 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0887 AC: 308 AN: 3472

East Asian (EAS) AF: 0.304 AC: 1567 AN: 5158

South Asian (SAS) AF: 0.153 AC: 738 AN: 4814

European-Finnish (FIN) AF: 0.0925 AC: 980 AN: 10594

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.158 AC: 10722 AN: 67972

Other (OTH) AF: 0.129 AC: 272 AN: 2110

Alfa AF: 0.0993 Hom.: 421

Bravo AF: 0.112

Asia WGS AF: 0.213 AC: 740 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.57
CADD	Benign	12
DANN	Benign	0.58
PhyloP100		5.9

Splicing

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

Other links and lift over

dbSNP: rs17279573; hg19: chr4-154580288;