7-99748750-C-T

Variant names:

• chr7-99748750-C-T
• rs2005548

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 0.0325 in 150,956 control chromosomes in the GnomAD database, including 354 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 0.033 (354 hom., cov: 32)
• Consequence: CYP3AP2 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.07
• Publications: 3 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.231 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: 0.0325 AC: 4908 AN: 150844 Hom.: 355 Cov.: 32

Gnomad AFR AF: 0.0282

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0683

Gnomad ASJ AF: 0.0115

Gnomad EAS AF: 0.243

Gnomad SAS AF: 0.236

Gnomad FIN AF: 0.000395

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.00313

Gnomad OTH AF: 0.0335

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

GnomAD4 genome AF: 0.0325 AC: 4913 AN: 150956 Hom.: 354 Cov.: 32 AF XY: 0.0388 AC XY: 2857 AN XY: 73658

African (AFR) AF: 0.0283 AC: 1164 AN: 41158

American (AMR) AF: 0.0685 AC: 1042 AN: 15212

Ashkenazi Jewish (ASJ) AF: 0.0115 AC: 40 AN: 3468

East Asian (EAS) AF: 0.243 AC: 1249 AN: 5150

South Asian (SAS) AF: 0.235 AC: 1130 AN: 4802

European-Finnish (FIN) AF: 0.000395 AC: 4 AN: 10128

Middle Eastern (MID) AF: 0.00340 AC: 1 AN: 294

European-Non Finnish (NFE) AF: 0.00313 AC: 212 AN: 67722

Other (OTH) AF: 0.0336 AC: 71 AN: 2110

Alfa AF: 0.0122 Hom.: 80

Bravo AF: 0.0336

Asia WGS AF: 0.232 AC: 804 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.0
DANN	Benign	0.59
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs2005548; hg19: chr7-99346373;