rs1224438

Variant names:

• chr12-45004258-A-C
• rs1224438

Your query was ambiguous. Multiple possible variants found:

• chr12-45004258-A-C
• chr12-45004258-A-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 0.715 in 151,908 control chromosomes in the GnomAD database, including 40,118 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 0.72 (40118 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.253
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.919 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: 0.715 AC: 108513 AN: 151790 Hom.: 40052 Cov.: 30

Gnomad AFR AF: 0.873

Gnomad AMI AF: 0.744

Gnomad AMR AF: 0.751

Gnomad ASJ AF: 0.586

Gnomad EAS AF: 0.941

Gnomad SAS AF: 0.846

Gnomad FIN AF: 0.644

Gnomad MID AF: 0.696

Gnomad NFE AF: 0.602

Gnomad OTH AF: 0.691

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

GnomAD4 genome AF: 0.715 AC: 108638 AN: 151908 Hom.: 40118 Cov.: 30 AF XY: 0.723 AC XY: 53700 AN XY: 74260

African (AFR) AF: 0.873 AC: 36194 AN: 41466

American (AMR) AF: 0.751 AC: 11446 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.586 AC: 2029 AN: 3464

East Asian (EAS) AF: 0.941 AC: 4848 AN: 5152

South Asian (SAS) AF: 0.846 AC: 4071 AN: 4814

European-Finnish (FIN) AF: 0.644 AC: 6797 AN: 10558

Middle Eastern (MID) AF: 0.680 AC: 200 AN: 294

European-Non Finnish (NFE) AF: 0.602 AC: 40910 AN: 67902

Other (OTH) AF: 0.694 AC: 1466 AN: 2112

Alfa AF: 0.641 Hom.: 38849

Bravo AF: 0.731

Asia WGS AF: 0.876 AC: 3044 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	4.4
DANN	Benign	0.71
PhyloP100		-0.25

Splicing

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

Other links and lift over

dbSNP: rs1224438; hg19: chr12-45398041;