rs4469412

Variant names:

• chr8-33707860-G-A
• rs4469412
• ENST00000523063.5:n.362-88434G>A

Variant summary

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

The ENST00000523063.5(ENSG00000253642):​n.362-88434G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0592 in 152,158 control chromosomes in the GnomAD database, including 401 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 0.059 (401 hom., cov: 32)
• Consequence: ENSG00000253642 ENST00000523063.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0480
• Publications: 5 publications found

Genes affected

ENSG00000253642 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.19 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000523063.5. 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
	ENSG00000253642	ENST00000523063.5	TSL:3	n.362-88434G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0592 AC: 8999 AN: 152038 Hom.: 400 Cov.: 32

Gnomad AFR AF: 0.0157

Gnomad AMI AF: 0.0538

Gnomad AMR AF: 0.0487

Gnomad ASJ AF: 0.0470

Gnomad EAS AF: 0.199

Gnomad SAS AF: 0.0645

Gnomad FIN AF: 0.0798

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0748

Gnomad OTH AF: 0.0536

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

GnomAD4 genome AF: 0.0592 AC: 9005 AN: 152158 Hom.: 401 Cov.: 32 AF XY: 0.0604 AC XY: 4494 AN XY: 74390

African (AFR) AF: 0.0157 AC: 652 AN: 41532

American (AMR) AF: 0.0488 AC: 745 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0470 AC: 163 AN: 3468

East Asian (EAS) AF: 0.200 AC: 1031 AN: 5164

South Asian (SAS) AF: 0.0650 AC: 313 AN: 4816

European-Finnish (FIN) AF: 0.0798 AC: 845 AN: 10584

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.0748 AC: 5084 AN: 67998

Other (OTH) AF: 0.0536 AC: 113 AN: 2110

Alfa AF: 0.0690 Hom.: 1785

Bravo AF: 0.0549

Asia WGS AF: 0.122 AC: 421 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.4
DANN	Benign	0.45
PhyloP100		0.048

Splicing

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

Other links and lift over

dbSNP: rs4469412; hg19: chr8-33565378;