rs4469428

Variant names:

• chr8-109062879-T-C
• rs4469428
• ENST00000522244.1:n.129+410A>G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000522244.1(ENSG00000253796):​n.129+410A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.672 in 152,108 control chromosomes in the GnomAD database, including 35,076 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 0.67 (35076 hom., cov: 32)
• Consequence: ENSG00000253796 ENST00000522244.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0880

Genes affected

ENSG00000253796 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.789 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
ENSG00000253796	ENST00000522244.1	n.129+410A>G		intron_variant	Intron 1 of 4	3

Frequencies

GnomAD3 genomes AF: 0.671 AC: 102038 AN: 151990 Hom.: 35033 Cov.: 32

Gnomad AFR AF: 0.796

Gnomad AMI AF: 0.732

Gnomad AMR AF: 0.749

Gnomad ASJ AF: 0.544

Gnomad EAS AF: 0.717

Gnomad SAS AF: 0.714

Gnomad FIN AF: 0.590

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.591

Gnomad OTH AF: 0.659

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

GnomAD4 genome AF: 0.672 AC: 102143 AN: 152108 Hom.: 35076 Cov.: 32 AF XY: 0.675 AC XY: 50205 AN XY: 74350

Gnomad4 AFR AF: 0.796

Gnomad4 AMR AF: 0.749

Gnomad4 ASJ AF: 0.544

Gnomad4 EAS AF: 0.718

Gnomad4 SAS AF: 0.714

Gnomad4 FIN AF: 0.590

Gnomad4 NFE AF: 0.591

Gnomad4 OTH AF: 0.660

Alfa AF: 0.643 Hom.: 5388

Bravo AF: 0.689

Asia WGS AF: 0.736 AC: 2559 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.4
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4469428; hg19: chr8-110075108;