rs12227938

Variant names:

• chr12-38240058-A-T
• rs12227938

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 0.236 in 152,110 control chromosomes in the GnomAD database, including 4,861 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 0.24 (4861 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.569
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.304 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: 0.236 AC: 35929 AN: 151992 Hom.: 4860 Cov.: 33

Gnomad AFR AF: 0.126

Gnomad AMI AF: 0.249

Gnomad AMR AF: 0.207

Gnomad ASJ AF: 0.298

Gnomad EAS AF: 0.147

Gnomad SAS AF: 0.153

Gnomad FIN AF: 0.308

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.308

Gnomad OTH AF: 0.268

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

GnomAD4 genome AF: 0.236 AC: 35921 AN: 152110 Hom.: 4861 Cov.: 33 AF XY: 0.233 AC XY: 17333 AN XY: 74358

African (AFR) AF: 0.125 AC: 5204 AN: 41530

American (AMR) AF: 0.206 AC: 3149 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.298 AC: 1035 AN: 3472

East Asian (EAS) AF: 0.147 AC: 757 AN: 5164

South Asian (SAS) AF: 0.152 AC: 734 AN: 4822

European-Finnish (FIN) AF: 0.308 AC: 3258 AN: 10568

Middle Eastern (MID) AF: 0.218 AC: 64 AN: 294

European-Non Finnish (NFE) AF: 0.308 AC: 20929 AN: 67976

Other (OTH) AF: 0.267 AC: 564 AN: 2116

Alfa AF: 0.276 Hom.: 810

Bravo AF: 0.225

Asia WGS AF: 0.155 AC: 541 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	4.1
DANN	Benign	0.53
PhyloP100		0.57

Splicing

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

Other links and lift over

dbSNP: rs12227938; hg19: chr12-38633860;