12-47944639-G-A

Variant names:

• chr12-47944639-G-A
• rs4547172

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 0.42 in 151,728 control chromosomes in the GnomAD database, including 15,705 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 0.42 (15705 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00600
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.74 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: 0.420 AC: 63608 AN: 151610 Hom.: 15671 Cov.: 32

Gnomad AFR AF: 0.639

Gnomad AMI AF: 0.320

Gnomad AMR AF: 0.490

Gnomad ASJ AF: 0.346

Gnomad EAS AF: 0.760

Gnomad SAS AF: 0.438

Gnomad FIN AF: 0.251

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.275

Gnomad OTH AF: 0.418

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

GnomAD4 genome AF: 0.420 AC: 63697 AN: 151728 Hom.: 15705 Cov.: 32 AF XY: 0.422 AC XY: 31299 AN XY: 74168

African (AFR) AF: 0.639 AC: 26390 AN: 41292

American (AMR) AF: 0.490 AC: 7483 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.346 AC: 1200 AN: 3464

East Asian (EAS) AF: 0.760 AC: 3923 AN: 5164

South Asian (SAS) AF: 0.436 AC: 2099 AN: 4812

European-Finnish (FIN) AF: 0.251 AC: 2641 AN: 10518

Middle Eastern (MID) AF: 0.330 AC: 97 AN: 294

European-Non Finnish (NFE) AF: 0.275 AC: 18688 AN: 67908

Other (OTH) AF: 0.420 AC: 886 AN: 2110

Alfa AF: 0.223 Hom.: 705

Bravo AF: 0.450

Asia WGS AF: 0.586 AC: 2031 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.1
DANN	Benign	0.29
PhyloP100		-0.0060

Splicing

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

Other links and lift over

dbSNP: rs4547172; hg19: chr12-48338422;