3-37402643-A-G

Position:

• chr3-37402643-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_171174.1(APRG1):​n.3526-8495A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.434 in 151,954 control chromosomes in the GnomAD database, including 15,004 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 0.43 (15004 hom., cov: 31)
• Consequence: APRG1 NR_171174.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.468

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.5 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
APRG1	NR_171174.1	n.3526-8495A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
APRG1	ENST00000662797.1	n.950+2984A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.434 AC: 65928 AN: 151836 Hom.: 14982 Cov.: 31

Gnomad AFR AF: 0.506

Gnomad AMI AF: 0.527

Gnomad AMR AF: 0.407

Gnomad ASJ AF: 0.364

Gnomad EAS AF: 0.0742

Gnomad SAS AF: 0.256

Gnomad FIN AF: 0.371

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.450

Gnomad OTH AF: 0.423

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

GnomAD4 genome AF: 0.434 AC: 65987 AN: 151954 Hom.: 15004 Cov.: 31 AF XY: 0.425 AC XY: 31589 AN XY: 74254

Gnomad4 AFR AF: 0.505

Gnomad4 AMR AF: 0.408

Gnomad4 ASJ AF: 0.364

Gnomad4 EAS AF: 0.0742

Gnomad4 SAS AF: 0.256

Gnomad4 FIN AF: 0.371

Gnomad4 NFE AF: 0.450

Gnomad4 OTH AF: 0.419

Alfa AF: 0.436 Hom.: 6907

Bravo AF: 0.442

Asia WGS AF: 0.189 AC: 657 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	0.71
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6772967; hg19: chr3-37444134;