3-37432765-T-C

Variant names:

• chr3-37432765-T-C
• rs1029236
• ENST00000328376.9:n.1206-2079T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000328376.9(APRG1):​n.1206-2079T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.424 in 151,308 control chromosomes in the GnomAD database, including 14,621 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 0.42 (14621 hom., cov: 29)
• Consequence: APRG1 ENST00000328376.9 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.55
• Publications: 6 publications found

Genes affected

APRG1 (HGNC:24082): (APRG1 tumor suppressor candidate) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.561 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
APRG1	NR_126512.1	n.974-2176T>C		intron_variant	Intron 6 of 6
APRG1	NR_126513.1	n.527-2176T>C		intron_variant	Intron 3 of 3
APRG1	NR_126514.1	n.527-2079T>C		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
APRG1	ENST00000328376.9	n.1206-2079T>C		intron_variant	Intron 5 of 5	1
APRG1	ENST00000332506.7	n.1289-2176T>C		intron_variant	Intron 6 of 6	1
APRG1	ENST00000466204.5	n.842-2176T>C		intron_variant	Intron 3 of 3	1

Frequencies

GnomAD3 genomes AF: 0.424 AC: 64094 AN: 151190 Hom.: 14606 Cov.: 29

Gnomad AFR AF: 0.567

Gnomad AMI AF: 0.561

Gnomad AMR AF: 0.335

Gnomad ASJ AF: 0.382

Gnomad EAS AF: 0.0265

Gnomad SAS AF: 0.254

Gnomad FIN AF: 0.343

Gnomad MID AF: 0.436

Gnomad NFE AF: 0.413

Gnomad OTH AF: 0.408

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

GnomAD4 genome AF: 0.424 AC: 64146 AN: 151308 Hom.: 14621 Cov.: 29 AF XY: 0.413 AC XY: 30536 AN XY: 73866

African (AFR) AF: 0.567 AC: 23316 AN: 41132

American (AMR) AF: 0.335 AC: 5076 AN: 15160

Ashkenazi Jewish (ASJ) AF: 0.382 AC: 1324 AN: 3464

East Asian (EAS) AF: 0.0261 AC: 134 AN: 5128

South Asian (SAS) AF: 0.253 AC: 1208 AN: 4776

European-Finnish (FIN) AF: 0.343 AC: 3591 AN: 10460

Middle Eastern (MID) AF: 0.421 AC: 123 AN: 292

European-Non Finnish (NFE) AF: 0.413 AC: 28017 AN: 67896

Other (OTH) AF: 0.405 AC: 845 AN: 2088

Alfa AF: 0.412 Hom.: 55748

Bravo AF: 0.432

Asia WGS AF: 0.150 AC: 522 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.082
DANN	Benign	0.28
PhyloP100		-1.5
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs1029236; hg19: chr3-37474256;