rs4572894

Variant names:

• chr4-122551631-A-G
• rs4572894

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 0.215 in 152,138 control chromosomes in the GnomAD database, including 3,894 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 0.22 (3894 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0850

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.273 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: 0.215 AC: 32741 AN: 152018 Hom.: 3894 Cov.: 32

Gnomad AFR AF: 0.148

Gnomad AMI AF: 0.414

Gnomad AMR AF: 0.190

Gnomad ASJ AF: 0.298

Gnomad EAS AF: 0.138

Gnomad SAS AF: 0.162

Gnomad FIN AF: 0.140

Gnomad MID AF: 0.194

Gnomad NFE AF: 0.276

Gnomad OTH AF: 0.233

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

GnomAD4 genome AF: 0.215 AC: 32750 AN: 152138 Hom.: 3894 Cov.: 32 AF XY: 0.207 AC XY: 15374 AN XY: 74364

Gnomad4 AFR AF: 0.147

Gnomad4 AMR AF: 0.190

Gnomad4 ASJ AF: 0.298

Gnomad4 EAS AF: 0.138

Gnomad4 SAS AF: 0.163

Gnomad4 FIN AF: 0.140

Gnomad4 NFE AF: 0.276

Gnomad4 OTH AF: 0.231

Alfa AF: 0.221 Hom.: 685

Bravo AF: 0.217

Asia WGS AF: 0.167 AC: 582 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	6.4
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4572894; hg19: chr4-123472786;