rs4074670

chr5-178777458-G-A

Variant summary

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

The NR_024035.2(AACSP1):n.648-1182C>T 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 0.185 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 NR_024035.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.50

Genes affected

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

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 (SAS) allele frequency at 95% confidence interval = 0.23 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
AACSP1	NR_024035.2	n.648-1182C>T		intron_variant, non_coding_transcript_variant
AACSP1	NR_135095.1	n.648-1182C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
AACSP1	ENST00000503486.6	n.648-1182C>T		intron_variant, non_coding_transcript_variant		1
AACSP1	ENST00000521412.2	n.640-2122C>T		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.0727

Gnomad4 AMR AF: 0.183

Gnomad4 ASJ AF: 0.251

Gnomad4 EAS AF: 0.168

Gnomad4 SAS AF: 0.238

Gnomad4 FIN AF: 0.279

Gnomad4 NFE AF: 0.233

Gnomad4 OTH AF: 0.200

Alfa AF: 0.225 Hom.: 7987

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4074670; hg19: chr5-178204459;