rs12705846

Variant names:

• chr7-113088952-A-G
• rs12705846

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 0.327 in 152,000 control chromosomes in the GnomAD database, including 8,684 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 0.33 (8684 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0990
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.393 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.327 AC: 49636 AN: 151882 Hom.: 8678 Cov.: 32

Gnomad AFR AF: 0.229

Gnomad AMI AF: 0.323

Gnomad AMR AF: 0.331

Gnomad ASJ AF: 0.462

Gnomad EAS AF: 0.0484

Gnomad SAS AF: 0.291

Gnomad FIN AF: 0.350

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.397

Gnomad OTH AF: 0.363

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

GnomAD4 genome AF: 0.327 AC: 49668 AN: 152000 Hom.: 8684 Cov.: 32 AF XY: 0.322 AC XY: 23932 AN XY: 74306

African (AFR) AF: 0.229 AC: 9481 AN: 41460

American (AMR) AF: 0.331 AC: 5048 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.462 AC: 1603 AN: 3470

East Asian (EAS) AF: 0.0482 AC: 250 AN: 5192

South Asian (SAS) AF: 0.290 AC: 1396 AN: 4816

European-Finnish (FIN) AF: 0.350 AC: 3692 AN: 10554

Middle Eastern (MID) AF: 0.456 AC: 134 AN: 294

European-Non Finnish (NFE) AF: 0.397 AC: 26993 AN: 67924

Other (OTH) AF: 0.368 AC: 778 AN: 2112

Alfa AF: 0.348 Hom.: 1466

Bravo AF: 0.321

Asia WGS AF: 0.214 AC: 743 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.57
DANN	Benign	0.70
PhyloP100		-0.099

Splicing

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

Other links and lift over

dbSNP: rs12705846; hg19: chr7-112729007;