9-37908661-G-A

Variant names:

• chr9-37908661-G-A
• rs3761672
• ENST00000540557.1:n.*560-8711C>T

Variant summary

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

The ENST00000540557.1(ENSG00000255872):​n.*560-8711C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.552 in 151,950 control chromosomes in the GnomAD database, including 23,726 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 0.55 (23726 hom., cov: 32)
• Consequence: ENSG00000255872 ENST00000540557.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.870
• Publications: 3 publications found

Genes affected

ENSG00000255872 (HGNC:):

PAICSP1 (HGNC:8588): (phosphoribosylaminoimidazole carboxylase, phosphoribosylaminoimidazole succinocarboxamide synthetase pseudogene 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.651 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PAICSP1		n.37908661G>A		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000255872	ENST00000540557.1	n.*560-8711C>T		intron_variant	Intron 6 of 11	5		ENSP00000457548.1

Frequencies

GnomAD3 genomes AF: 0.552 AC: 83759 AN: 151832 Hom.: 23661 Cov.: 32

Gnomad AFR AF: 0.657

Gnomad AMI AF: 0.576

Gnomad AMR AF: 0.587

Gnomad ASJ AF: 0.432

Gnomad EAS AF: 0.573

Gnomad SAS AF: 0.644

Gnomad FIN AF: 0.513

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.484

Gnomad OTH AF: 0.548

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

GnomAD4 genome AF: 0.552 AC: 83886 AN: 151950 Hom.: 23726 Cov.: 32 AF XY: 0.553 AC XY: 41056 AN XY: 74262

African (AFR) AF: 0.657 AC: 27234 AN: 41432

American (AMR) AF: 0.588 AC: 8982 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.432 AC: 1495 AN: 3462

East Asian (EAS) AF: 0.572 AC: 2955 AN: 5166

South Asian (SAS) AF: 0.644 AC: 3104 AN: 4818

European-Finnish (FIN) AF: 0.513 AC: 5400 AN: 10532

Middle Eastern (MID) AF: 0.452 AC: 133 AN: 294

European-Non Finnish (NFE) AF: 0.484 AC: 32893 AN: 67952

Other (OTH) AF: 0.552 AC: 1165 AN: 2110

Alfa AF: 0.508 Hom.: 10337

Bravo AF: 0.564

Asia WGS AF: 0.636 AC: 2213 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	5.7
DANN	Benign	0.46
PhyloP100		0.87

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: rs3761672; hg19: chr9-37908658; COSMIC: COSV54252535;