rs12233759

Variant names:

• chr4-89959252-G-A
• rs12233759

Your query was ambiguous. Multiple possible variants found:

• chr4-89959252-G-A
• chr4-89959252-G-C
• chr4-89959252-G-T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.533 AC: 22102 AN: 41476

American (AMR) AF: 0.302 AC: 4607 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.288 AC: 1001 AN: 3472

East Asian (EAS) AF: 0.651 AC: 3375 AN: 5184

South Asian (SAS) AF: 0.372 AC: 1792 AN: 4822

European-Finnish (FIN) AF: 0.247 AC: 2613 AN: 10570

Middle Eastern (MID) AF: 0.364 AC: 107 AN: 294

European-Non Finnish (NFE) AF: 0.197 AC: 13398 AN: 67976

Other (OTH) AF: 0.330 AC: 698 AN: 2112

Alfa AF: 0.241 Hom.: 14873

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
PhyloP100		-0.82

Splicing

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

Other links and lift over

dbSNP: rs12233759; hg19: chr4-90880403;