rs4074670

Variant names:

• chr5-178777458-G-A
• rs4074670
• ENST00000503486.6:n.648-1182C>T

Variant summary

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

The ENST00000503486.6(AACSP1):​n.648-1182C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.185 in 152,102 control chromosomes in the GnomAD database, including 3,066 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 0.19 (3066 hom., cov: 32)
• Consequence: AACSP1 ENST00000503486.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.50
• Publications: 1 publications found

Genes affected

AACSP1 (HGNC:):

AACSP1 (HGNC:18226): (acetoacetyl-CoA synthetase pseudogene 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.23 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
AACSP1	NR_024035.2	n.648-1182C>T		intron_variant	Intron 4 of 10
AACSP1	NR_135095.1	n.648-1182C>T		intron_variant	Intron 4 of 10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
AACSP1	ENST00000503486.6	n.648-1182C>T		intron_variant	Intron 4 of 10	1
AACSP1	ENST00000521412.3	n.632-2122C>T		intron_variant	Intron 7 of 10	6

Frequencies

GnomAD3 genomes AF: 0.186 AC: 28198 AN: 151984 Hom.: 3069 Cov.: 32

Gnomad AFR AF: 0.0727

Gnomad AMI AF: 0.267

Gnomad AMR AF: 0.183

Gnomad ASJ AF: 0.251

Gnomad EAS AF: 0.168

Gnomad SAS AF: 0.240

Gnomad FIN AF: 0.279

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.233

Gnomad OTH AF: 0.197

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

GnomAD4 genome AF: 0.185 AC: 28199 AN: 152102 Hom.: 3066 Cov.: 32 AF XY: 0.188 AC XY: 14009 AN XY: 74334

African (AFR) AF: 0.0727 AC: 3019 AN: 41526

American (AMR) AF: 0.183 AC: 2797 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.251 AC: 872 AN: 3470

East Asian (EAS) AF: 0.168 AC: 866 AN: 5158

South Asian (SAS) AF: 0.238 AC: 1147 AN: 4820

European-Finnish (FIN) AF: 0.279 AC: 2945 AN: 10546

Middle Eastern (MID) AF: 0.255 AC: 75 AN: 294

European-Non Finnish (NFE) AF: 0.233 AC: 15814 AN: 67982

Other (OTH) AF: 0.200 AC: 422 AN: 2114

Alfa AF: 0.216 Hom.: 11529

Bravo AF: 0.173

Asia WGS AF: 0.207 AC: 720 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	0.48
DANN	Benign	0.64
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs4074670; hg19: chr5-178204459;