rs4469431

Variant names:

• chr8-56273474-G-A
• rs4469431

Variant summary

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

The variant allele was found at a frequency of 0.158 in 152,142 control chromosomes in the GnomAD database, including 1,966 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 0.16 (1966 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.913

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.207 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

Frequencies

GnomAD3 genomes AF: 0.158 AC: 24028 AN: 152024 Hom.: 1961 Cov.: 32

Gnomad AFR AF: 0.210

Gnomad AMI AF: 0.123

Gnomad AMR AF: 0.162

Gnomad ASJ AF: 0.193

Gnomad EAS AF: 0.0605

Gnomad SAS AF: 0.139

Gnomad FIN AF: 0.133

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.136

Gnomad OTH AF: 0.174

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

GnomAD4 genome AF: 0.158 AC: 24050 AN: 152142 Hom.: 1966 Cov.: 32 AF XY: 0.156 AC XY: 11605 AN XY: 74376

Gnomad4 AFR AF: 0.211

Gnomad4 AMR AF: 0.162

Gnomad4 ASJ AF: 0.193

Gnomad4 EAS AF: 0.0603

Gnomad4 SAS AF: 0.138

Gnomad4 FIN AF: 0.133

Gnomad4 NFE AF: 0.136

Gnomad4 OTH AF: 0.173

Alfa AF: 0.124 Hom.: 175

Asia WGS AF: 0.133 AC: 462 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.6
DANN	Benign	0.28

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4469431; hg19: chr8-57186033;