chr12-25251670-G-A

Variant names:

• chr12-25251670-G-A
• rs7312175

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 0.153 in 152,116 control chromosomes in the GnomAD database, including 1,874 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 0.15 (1874 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.16
• Publications: 19 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.165 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: 0.153 AC: 23300 AN: 151998 Hom.: 1864 Cov.: 32

Gnomad AFR AF: 0.162

Gnomad AMI AF: 0.0998

Gnomad AMR AF: 0.170

Gnomad ASJ AF: 0.0548

Gnomad EAS AF: 0.0993

Gnomad SAS AF: 0.120

Gnomad FIN AF: 0.251

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.142

Gnomad OTH AF: 0.124

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

GnomAD4 genome AF: 0.153 AC: 23326 AN: 152116 Hom.: 1874 Cov.: 32 AF XY: 0.158 AC XY: 11726 AN XY: 74352

African (AFR) AF: 0.163 AC: 6746 AN: 41480

American (AMR) AF: 0.170 AC: 2604 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0548 AC: 190 AN: 3470

East Asian (EAS) AF: 0.0995 AC: 515 AN: 5176

South Asian (SAS) AF: 0.120 AC: 576 AN: 4820

European-Finnish (FIN) AF: 0.251 AC: 2656 AN: 10566

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.142 AC: 9668 AN: 67984

Other (OTH) AF: 0.123 AC: 260 AN: 2114

Alfa AF: 0.150 Hom.: 649

Bravo AF: 0.149

Asia WGS AF: 0.0930 AC: 322 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.62
DANN	Benign	0.63
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs7312175; hg19: chr12-25404604;