chr7-12188266-A-G

Variant names:

• chr7-12188266-A-G
• rs1468915

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 0.198 in 152,072 control chromosomes in the GnomAD database, including 3,379 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 0.20 (3379 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.33
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.334 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.198 AC: 30053 AN: 151954 Hom.: 3384 Cov.: 32

Gnomad AFR AF: 0.0859

Gnomad AMI AF: 0.159

Gnomad AMR AF: 0.254

Gnomad ASJ AF: 0.239

Gnomad EAS AF: 0.347

Gnomad SAS AF: 0.333

Gnomad FIN AF: 0.206

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.229

Gnomad OTH AF: 0.203

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

GnomAD4 genome AF: 0.198 AC: 30053 AN: 152072 Hom.: 3379 Cov.: 32 AF XY: 0.202 AC XY: 15018 AN XY: 74310

African (AFR) AF: 0.0858 AC: 3563 AN: 41530

American (AMR) AF: 0.254 AC: 3874 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.239 AC: 829 AN: 3468

East Asian (EAS) AF: 0.347 AC: 1792 AN: 5160

South Asian (SAS) AF: 0.332 AC: 1596 AN: 4814

European-Finnish (FIN) AF: 0.206 AC: 2181 AN: 10580

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.229 AC: 15568 AN: 67940

Other (OTH) AF: 0.205 AC: 432 AN: 2112

Alfa AF: 0.226 Hom.: 5616

Bravo AF: 0.192

Asia WGS AF: 0.312 AC: 1083 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	6.3
DANN	Benign	0.76
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs1468915; hg19: chr7-12227892;