rs4862633

chr4-186088818-T-C

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 0.769 in 152,174 control chromosomes in the GnomAD database, including 45,261 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 0.77 (45261 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.542

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.859 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: 0.769 AC: 116961 AN: 152054 Hom.: 45234 Cov.: 33

Gnomad AFR AF: 0.749

Gnomad AMI AF: 0.740

Gnomad AMR AF: 0.821

Gnomad ASJ AF: 0.603

Gnomad EAS AF: 0.881

Gnomad SAS AF: 0.722

Gnomad FIN AF: 0.865

Gnomad MID AF: 0.703

Gnomad NFE AF: 0.759

Gnomad OTH AF: 0.755

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

GnomAD4 genome AF: 0.769 AC: 117038 AN: 152174 Hom.: 45261 Cov.: 33 AF XY: 0.775 AC XY: 57649 AN XY: 74396

Gnomad4 AFR AF: 0.749

Gnomad4 AMR AF: 0.822

Gnomad4 ASJ AF: 0.603

Gnomad4 EAS AF: 0.881

Gnomad4 SAS AF: 0.721

Gnomad4 FIN AF: 0.865

Gnomad4 NFE AF: 0.759

Gnomad4 OTH AF: 0.755

Alfa AF: 0.753 Hom.: 69174

Bravo AF: 0.767

Asia WGS AF: 0.801 AC: 2784 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	3.0
Dann	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4862633; hg19: chr4-187009972;