ENST00000521433.1:n.179+32046T>G

Variant names:

• chr8-88361098-T-G
• rs36116061
• ENST00000521433.1:n.179+32046T>G

Variant summary

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

The ENST00000521433.1(ENSG00000253553):​n.179+32046T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.203 in 151,706 control chromosomes in the GnomAD database, including 3,259 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 0.20 (3259 hom., cov: 31)
• Consequence: ENSG00000253553 ENST00000521433.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00
• Publications: 2 publications found

Genes affected

ENSG00000253553 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.218 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000521433.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000253553	ENST00000521433.1	TSL:4	n.179+32046T>G		intron	N/A
	ENSG00000253553	ENST00000658256.1		n.284+32001T>G		intron	N/A
	ENSG00000253553	ENST00000658283.1		n.425+32102T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.203 AC: 30824 AN: 151590 Hom.: 3245 Cov.: 31

Gnomad AFR AF: 0.210

Gnomad AMI AF: 0.357

Gnomad AMR AF: 0.219

Gnomad ASJ AF: 0.161

Gnomad EAS AF: 0.0507

Gnomad SAS AF: 0.230

Gnomad FIN AF: 0.195

Gnomad MID AF: 0.163

Gnomad NFE AF: 0.206

Gnomad OTH AF: 0.219

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

GnomAD4 genome AF: 0.203 AC: 30871 AN: 151706 Hom.: 3259 Cov.: 31 AF XY: 0.202 AC XY: 14967 AN XY: 74182

African (AFR) AF: 0.211 AC: 8713 AN: 41374

American (AMR) AF: 0.219 AC: 3336 AN: 15210

Ashkenazi Jewish (ASJ) AF: 0.161 AC: 559 AN: 3468

East Asian (EAS) AF: 0.0506 AC: 262 AN: 5176

South Asian (SAS) AF: 0.229 AC: 1097 AN: 4792

European-Finnish (FIN) AF: 0.195 AC: 2048 AN: 10478

Middle Eastern (MID) AF: 0.172 AC: 50 AN: 290

European-Non Finnish (NFE) AF: 0.206 AC: 14008 AN: 67906

Other (OTH) AF: 0.225 AC: 474 AN: 2104

Alfa AF: 0.183 Hom.: 1381

Bravo AF: 0.204

Asia WGS AF: 0.195 AC: 675 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.61
DANN	Benign	0.33
PhyloP100		0.0

Splicing

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

Other links and lift over

dbSNP: rs36116061; hg19: chr8-89373327;