rs2514037

Variant names:

• chr11-67648719-C-T
• rs2514037
• NM_080658.2:c.-94-1130G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 9 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
ACY3	NM_080658.2	c.-94-1130G>A		intron_variant	Intron 1 of 7	ENST00000255082.8	NP_542389.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ACY3	ENST00000255082.8	c.-94-1130G>A		intron_variant	Intron 1 of 7	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

African (AFR) AF: 0.209 AC: 8695 AN: 41520

American (AMR) AF: 0.0989 AC: 1513 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.0669 AC: 232 AN: 3470

East Asian (EAS) AF: 0.128 AC: 660 AN: 5158

South Asian (SAS) AF: 0.0390 AC: 188 AN: 4826

European-Finnish (FIN) AF: 0.0808 AC: 858 AN: 10620

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.103 AC: 6999 AN: 67982

Other (OTH) AF: 0.123 AC: 260 AN: 2114

Alfa AF: 0.109 Hom.: 1781

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
PhyloP100		-0.043
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2514037; hg19: chr11-67416190;