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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CYP3AP2		n.99750705T>C		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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 v4.3

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;