rs12228387

Variant names:

• chr12-118964738-G-A
• rs12228387

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 0.0478 in 152,202 control chromosomes in the GnomAD database, including 255 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 0.048 (255 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.331
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.139 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: 0.0478 AC: 7267 AN: 152084 Hom.: 255 Cov.: 32

Gnomad AFR AF: 0.0126

Gnomad AMI AF: 0.0428

Gnomad AMR AF: 0.0328

Gnomad ASJ AF: 0.0121

Gnomad EAS AF: 0.148

Gnomad SAS AF: 0.0435

Gnomad FIN AF: 0.111

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0575

Gnomad OTH AF: 0.0464

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

GnomAD4 genome AF: 0.0478 AC: 7275 AN: 152202 Hom.: 255 Cov.: 32 AF XY: 0.0498 AC XY: 3702 AN XY: 74398

African (AFR) AF: 0.0126 AC: 525 AN: 41538

American (AMR) AF: 0.0333 AC: 510 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0121 AC: 42 AN: 3470

East Asian (EAS) AF: 0.147 AC: 759 AN: 5150

South Asian (SAS) AF: 0.0435 AC: 210 AN: 4824

European-Finnish (FIN) AF: 0.111 AC: 1175 AN: 10586

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.0575 AC: 3910 AN: 68020

Other (OTH) AF: 0.0464 AC: 98 AN: 2114

Alfa AF: 0.0524 Hom.: 437

Bravo AF: 0.0428

Asia WGS AF: 0.0750 AC: 258 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.3
DANN	Benign	0.44
PhyloP100		0.33

Splicing

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

Other links and lift over

dbSNP: rs12228387; hg19: chr12-119402543;