8-33017609-T-A

Variant names:

• chr8-33017609-T-A
• rs4733142
• ENST00000500843.2:n.139+21293T>A

Variant summary

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

The ENST00000500843.2(ENSG00000247134):​n.139+21293T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.418 in 151,926 control chromosomes in the GnomAD database, including 14,781 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 0.42 (14781 hom., cov: 32)
• Consequence: ENSG00000247134 ENST00000500843.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.972
• Publications: 1 publications found

Genes affected

ENSG00000247134 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.95 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000500843.2. 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
	LOC105379362	NR_188148.1		n.272+21254T>A		intron	N/A
	LOC105379362	NR_188149.1		n.118-24026T>A		intron	N/A
	LOC105379362	NR_188150.1		n.118-24026T>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000247134	ENST00000500843.2	TSL:5	n.139+21293T>A		intron	N/A
	ENSG00000247134	ENST00000520819.6	TSL:2	n.139+21293T>A		intron	N/A
	ENSG00000247134	ENST00000655535.1		n.230+21293T>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.418 AC: 63384 AN: 151808 Hom.: 14762 Cov.: 32

Gnomad AFR AF: 0.304

Gnomad AMI AF: 0.445

Gnomad AMR AF: 0.551

Gnomad ASJ AF: 0.462

Gnomad EAS AF: 0.972

Gnomad SAS AF: 0.648

Gnomad FIN AF: 0.304

Gnomad MID AF: 0.491

Gnomad NFE AF: 0.411

Gnomad OTH AF: 0.459

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

GnomAD4 genome AF: 0.418 AC: 63442 AN: 151926 Hom.: 14781 Cov.: 32 AF XY: 0.423 AC XY: 31407 AN XY: 74254

African (AFR) AF: 0.304 AC: 12611 AN: 41426

American (AMR) AF: 0.552 AC: 8401 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.462 AC: 1603 AN: 3468

East Asian (EAS) AF: 0.972 AC: 5018 AN: 5162

South Asian (SAS) AF: 0.647 AC: 3123 AN: 4824

European-Finnish (FIN) AF: 0.304 AC: 3211 AN: 10566

Middle Eastern (MID) AF: 0.480 AC: 141 AN: 294

European-Non Finnish (NFE) AF: 0.411 AC: 27952 AN: 67938

Other (OTH) AF: 0.463 AC: 977 AN: 2108

Alfa AF: 0.403 Hom.: 1627

Bravo AF: 0.433

Asia WGS AF: 0.760 AC: 2638 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.6
DANN	Benign	0.26
PhyloP100		-0.97

Splicing

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

Other links and lift over

dbSNP: rs4733142; hg19: chr8-32875127;