rs7012225

Variant names:

• chr8-109074626-A-G
• rs7012225

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 0.208 in 152,126 control chromosomes in the GnomAD database, including 3,586 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 0.21 (3586 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.76

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.33 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: 0.208 AC: 31626 AN: 152006 Hom.: 3581 Cov.: 32

Gnomad AFR AF: 0.210

Gnomad AMI AF: 0.0789

Gnomad AMR AF: 0.337

Gnomad ASJ AF: 0.134

Gnomad EAS AF: 0.0580

Gnomad SAS AF: 0.124

Gnomad FIN AF: 0.215

Gnomad MID AF: 0.166

Gnomad NFE AF: 0.200

Gnomad OTH AF: 0.227

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

GnomAD4 genome AF: 0.208 AC: 31655 AN: 152126 Hom.: 3586 Cov.: 32 AF XY: 0.210 AC XY: 15596 AN XY: 74356

Gnomad4 AFR AF: 0.209

Gnomad4 AMR AF: 0.338

Gnomad4 ASJ AF: 0.134

Gnomad4 EAS AF: 0.0583

Gnomad4 SAS AF: 0.124

Gnomad4 FIN AF: 0.215

Gnomad4 NFE AF: 0.200

Gnomad4 OTH AF: 0.226

Alfa AF: 0.211 Hom.: 907

Bravo AF: 0.215

Asia WGS AF: 0.0880 AC: 307 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	5.5
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7012225; hg19: chr8-110086855;