11-67648719-C-T

Position:

• chr11-67648719-C-T

Variant summary

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

The NM_080658.2(ACY3):​c.-94-1130G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.129 in 152,198 control chromosomes in the GnomAD database, including 1,502 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 0.13 (1502 hom., cov: 33)
• Consequence: ACY3 NM_080658.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0430

Genes affected

ACY3 (HGNC:24104): (aminoacylase 3) Predicted to enable aminoacylase activity. Located in extracellular exosome. [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=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.206 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ACY3	NM_080658.2	c.-94-1130G>A		intron_variant		ENST00000255082.8	NP_542389.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ACY3	ENST00000255082.8	c.-94-1130G>A		intron_variant		1	NM_080658.2	ENSP00000255082.3

Frequencies

GnomAD3 genomes AF: 0.129 AC: 19556 AN: 152080 Hom.: 1503 Cov.: 33

Gnomad AFR AF: 0.210

Gnomad AMI AF: 0.159

Gnomad AMR AF: 0.0990

Gnomad ASJ AF: 0.0669

Gnomad EAS AF: 0.128

Gnomad SAS AF: 0.0400

Gnomad FIN AF: 0.0808

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.103

Gnomad OTH AF: 0.124

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

GnomAD4 genome AF: 0.129 AC: 19571 AN: 152198 Hom.: 1502 Cov.: 33 AF XY: 0.127 AC XY: 9413 AN XY: 74396

Gnomad4 AFR AF: 0.209

Gnomad4 AMR AF: 0.0989

Gnomad4 ASJ AF: 0.0669

Gnomad4 EAS AF: 0.128

Gnomad4 SAS AF: 0.0390

Gnomad4 FIN AF: 0.0808

Gnomad4 NFE AF: 0.103

Gnomad4 OTH AF: 0.123

Alfa AF: 0.108 Hom.: 1066

Bravo AF: 0.134

Asia WGS AF: 0.0980 AC: 343 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.6
DANN	Benign	0.61

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs2514037; hg19: chr11-67416190;