rs4573528

chr1-222455181-T-G

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;