rs574666

Variant names:

• chr4-20235227-C-T
• rs574666

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 0.682 in 152,040 control chromosomes in the GnomAD database, including 35,785 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 0.68 (35785 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0590

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.95 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: 0.682 AC: 103611 AN: 151922 Hom.: 35774 Cov.: 32

Gnomad AFR AF: 0.596

Gnomad AMI AF: 0.643

Gnomad AMR AF: 0.786

Gnomad ASJ AF: 0.795

Gnomad EAS AF: 0.972

Gnomad SAS AF: 0.792

Gnomad FIN AF: 0.665

Gnomad MID AF: 0.768

Gnomad NFE AF: 0.677

Gnomad OTH AF: 0.713

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

GnomAD4 genome AF: 0.682 AC: 103659 AN: 152040 Hom.: 35785 Cov.: 32 AF XY: 0.688 AC XY: 51149 AN XY: 74324

Gnomad4 AFR AF: 0.596

Gnomad4 AMR AF: 0.786

Gnomad4 ASJ AF: 0.795

Gnomad4 EAS AF: 0.972

Gnomad4 SAS AF: 0.791

Gnomad4 FIN AF: 0.665

Gnomad4 NFE AF: 0.677

Gnomad4 OTH AF: 0.718

Alfa AF: 0.677 Hom.: 4490

Bravo AF: 0.690

Asia WGS AF: 0.858 AC: 2982 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	6.0
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs574666; hg19: chr4-20236850; COSMIC: COSV53465233;