ENST00000522189.1:n.22-141098G>A

Variant names:

• chr5-165636879-G-A
• rs958994
• ENST00000522189.1:n.22-141098G>A

Variant summary

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

The ENST00000522189.1(ENSG00000253693):​n.22-141098G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.729 in 151,914 control chromosomes in the GnomAD database, including 40,467 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 0.73 (40467 hom., cov: 32)
• Consequence: ENSG00000253693 ENST00000522189.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.356
• Publications: 12 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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.808 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000522189.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000253693	ENST00000522189.1	TSL:5	n.22-141098G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.729 AC: 110642 AN: 151796 Hom.: 40437 Cov.: 32

Gnomad AFR AF: 0.779

Gnomad AMI AF: 0.680

Gnomad AMR AF: 0.743

Gnomad ASJ AF: 0.739

Gnomad EAS AF: 0.829

Gnomad SAS AF: 0.717

Gnomad FIN AF: 0.628

Gnomad MID AF: 0.750

Gnomad NFE AF: 0.704

Gnomad OTH AF: 0.744

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

GnomAD4 genome AF: 0.729 AC: 110719 AN: 151914 Hom.: 40467 Cov.: 32 AF XY: 0.725 AC XY: 53840 AN XY: 74218

African (AFR) AF: 0.779 AC: 32312 AN: 41496

American (AMR) AF: 0.743 AC: 11326 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.739 AC: 2565 AN: 3470

East Asian (EAS) AF: 0.829 AC: 4270 AN: 5150

South Asian (SAS) AF: 0.716 AC: 3454 AN: 4824

European-Finnish (FIN) AF: 0.628 AC: 6609 AN: 10528

Middle Eastern (MID) AF: 0.752 AC: 221 AN: 294

European-Non Finnish (NFE) AF: 0.704 AC: 47783 AN: 67886

Other (OTH) AF: 0.738 AC: 1559 AN: 2112

Alfa AF: 0.715 Hom.: 95327

Bravo AF: 0.741

Asia WGS AF: 0.773 AC: 2685 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.4
DANN	Benign	0.57
PhyloP100		-0.36

Splicing

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

Other links and lift over

dbSNP: rs958994; hg19: chr5-165063884;