ENST00000522189.1:n.22-153652G>A

Variant names:

• chr5-165624325-G-A
• rs1030154
• ENST00000522189.1:n.22-153652G>A

Variant summary

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

The ENST00000522189.1(ENSG00000253693):​n.22-153652G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.195 in 152,014 control chromosomes in the GnomAD database, including 3,067 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 0.19 (3067 hom., cov: 32)
• Consequence: ENSG00000253693 ENST00000522189.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.993
• Publications: 4 publications found

Genes affected

ENSG00000253693 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.406 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000253693	ENST00000522189.1	n.22-153652G>A		intron_variant	Intron 1 of 1	5

Frequencies

GnomAD3 genomes AF: 0.195 AC: 29551 AN: 151894 Hom.: 3063 Cov.: 32

Gnomad AFR AF: 0.169

Gnomad AMI AF: 0.129

Gnomad AMR AF: 0.154

Gnomad ASJ AF: 0.201

Gnomad EAS AF: 0.420

Gnomad SAS AF: 0.184

Gnomad FIN AF: 0.275

Gnomad MID AF: 0.156

Gnomad NFE AF: 0.192

Gnomad OTH AF: 0.185

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

GnomAD4 genome AF: 0.195 AC: 29585 AN: 152014 Hom.: 3067 Cov.: 32 AF XY: 0.201 AC XY: 14924 AN XY: 74268

African (AFR) AF: 0.169 AC: 6997 AN: 41458

American (AMR) AF: 0.154 AC: 2346 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.201 AC: 697 AN: 3472

East Asian (EAS) AF: 0.420 AC: 2168 AN: 5158

South Asian (SAS) AF: 0.184 AC: 889 AN: 4826

European-Finnish (FIN) AF: 0.275 AC: 2895 AN: 10534

Middle Eastern (MID) AF: 0.171 AC: 50 AN: 292

European-Non Finnish (NFE) AF: 0.192 AC: 13035 AN: 67980

Other (OTH) AF: 0.185 AC: 390 AN: 2112

Alfa AF: 0.187 Hom.: 8607

Bravo AF: 0.187

Asia WGS AF: 0.271 AC: 947 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.66
PhyloP100		-0.99

Splicing

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

Other links and lift over

dbSNP: rs1030154; hg19: chr5-165051330;