rs7312175

Variant names:

• chr12-25251670-G-A
• rs7312175

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.163

Gnomad4 AMR AF: 0.170

Gnomad4 ASJ AF: 0.0548

Gnomad4 EAS AF: 0.0995

Gnomad4 SAS AF: 0.120

Gnomad4 FIN AF: 0.251

Gnomad4 NFE AF: 0.142

Gnomad4 OTH AF: 0.123

Alfa AF: 0.157 Hom.: 389

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7312175; hg19: chr12-25404604;