rs12233759

chr4-89959252-G-Achr4-89959252-G-Cchr4-89959252-G-T

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 0.328 in 152,098 control chromosomes in the GnomAD database, including 10,005 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 0.33 (10005 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.820

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.633 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: 0.328 AC: 49882 AN: 151980 Hom.: 9976 Cov.: 33

Gnomad AFR AF: 0.533

Gnomad AMI AF: 0.284

Gnomad AMR AF: 0.302

Gnomad ASJ AF: 0.288

Gnomad EAS AF: 0.651

Gnomad SAS AF: 0.372

Gnomad FIN AF: 0.247

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.197

Gnomad OTH AF: 0.324

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

GnomAD4 genome AF: 0.328 AC: 49952 AN: 152098 Hom.: 10005 Cov.: 33 AF XY: 0.332 AC XY: 24701 AN XY: 74362

Gnomad4 AFR AF: 0.533

Gnomad4 AMR AF: 0.302

Gnomad4 ASJ AF: 0.288

Gnomad4 EAS AF: 0.651

Gnomad4 SAS AF: 0.372

Gnomad4 FIN AF: 0.247

Gnomad4 NFE AF: 0.197

Gnomad4 OTH AF: 0.330

Alfa AF: 0.222 Hom.: 7882

Bravo AF: 0.341

Asia WGS AF: 0.507 AC: 1760 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	0.11
Dann	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12233759; hg19: chr4-90880403;