rs4573528

Variant names:

• chr1-222455181-T-G
• rs4573528

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.109 in 152,310 control chromosomes in the GnomAD database, including 1,073 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 0.11 (1073 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.159

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.38).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.177 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: 0.109 AC: 16534 AN: 152192 Hom.: 1072 Cov.: 33

Gnomad AFR AF: 0.181

Gnomad AMI AF: 0.130

Gnomad AMR AF: 0.0863

Gnomad ASJ AF: 0.0680

Gnomad EAS AF: 0.00558

Gnomad SAS AF: 0.0284

Gnomad FIN AF: 0.0736

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.0904

Gnomad OTH AF: 0.109

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

GnomAD4 genome AF: 0.109 AC: 16557 AN: 152310 Hom.: 1073 Cov.: 33 AF XY: 0.106 AC XY: 7888 AN XY: 74492

Gnomad4 AFR AF: 0.181

Gnomad4 AMR AF: 0.0861

Gnomad4 ASJ AF: 0.0680

Gnomad4 EAS AF: 0.00559

Gnomad4 SAS AF: 0.0290

Gnomad4 FIN AF: 0.0736

Gnomad4 NFE AF: 0.0904

Gnomad4 OTH AF: 0.108

Alfa AF: 0.0925 Hom.: 378

Bravo AF: 0.114

Asia WGS AF: 0.0430 AC: 151 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.38
CADD	Benign	15
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4573528; hg19: chr1-222628523;