rs6945984

Variant names:

• chr7-99750705-T-C
• rs6945984

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 0.303 in 152,162 control chromosomes in the GnomAD database, including 12,139 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 0.30 (12139 hom., cov: 32)
• Consequence: CYP3AP2 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.267
• Publications: 14 publications found

Genes affected

CYP3AP2 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.698 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.302 AC: 45951 AN: 152044 Hom.: 12100 Cov.: 32

Gnomad AFR AF: 0.704

Gnomad AMI AF: 0.0713

Gnomad AMR AF: 0.259

Gnomad ASJ AF: 0.116

Gnomad EAS AF: 0.299

Gnomad SAS AF: 0.351

Gnomad FIN AF: 0.109

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.108

Gnomad OTH AF: 0.276

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

GnomAD4 genome AF: 0.303 AC: 46050 AN: 152162 Hom.: 12139 Cov.: 32 AF XY: 0.303 AC XY: 22527 AN XY: 74416

African (AFR) AF: 0.705 AC: 29245 AN: 41488

American (AMR) AF: 0.259 AC: 3965 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.116 AC: 401 AN: 3466

East Asian (EAS) AF: 0.299 AC: 1550 AN: 5188

South Asian (SAS) AF: 0.350 AC: 1688 AN: 4818

European-Finnish (FIN) AF: 0.109 AC: 1157 AN: 10592

Middle Eastern (MID) AF: 0.211 AC: 62 AN: 294

European-Non Finnish (NFE) AF: 0.108 AC: 7331 AN: 67992

Other (OTH) AF: 0.277 AC: 586 AN: 2114

Alfa AF: 0.177 Hom.: 3326

Bravo AF: 0.328

Asia WGS AF: 0.375 AC: 1303 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	5.2
DANN	Benign	0.59
PhyloP100		-0.27

Splicing

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

Other links and lift over

dbSNP: rs6945984; hg19: chr7-99348328;