rs7012225

Positions:

• chr8-109074626-A-G

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;