rs4469412

chr8-33707860-G-A

Variant summary

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

The ENST00000523063.5(ENSG00000253642):n.362-88434G>A variant causes a intron, non coding transcript 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: ENST00000523063.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0480

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000523063.5	n.362-88434G>A		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR AF: 0.0157

Gnomad4 AMR AF: 0.0488

Gnomad4 ASJ AF: 0.0470

Gnomad4 EAS AF: 0.200

Gnomad4 SAS AF: 0.0650

Gnomad4 FIN AF: 0.0798

Gnomad4 NFE AF: 0.0748

Gnomad4 OTH AF: 0.0536

Alfa AF: 0.0704 Hom.: 859

Bravo AF: 0.0549

Asia WGS AF: 0.122 AC: 421 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	1.4
Dann	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4469412; hg19: chr8-33565378;