11-34880331-G-C

Variant names:

• chr11-34880331-G-C
• rs2915228
• ENST00000532428.6:n.*41+2345C>G

Variant summary

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

The ENST00000532428.6(APIP):​n.*41+2345C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.564 in 152,038 control chromosomes in the GnomAD database, including 25,244 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 0.56 (25244 hom., cov: 32)
• Consequence: APIP ENST00000532428.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.152
• Publications: 7 publications found

Genes affected

APIP (HGNC:17581): (APAF1 interacting protein) Enables identical protein binding activity; methylthioribulose 1-phosphate dehydratase activity; and zinc ion binding activity. Involved in several processes, including L-methionine salvage from methylthioadenosine; protein homotetramerization; and pyroptosis. Located in cytoplasm. [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=-0.62).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.808 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
APIP	ENST00000532428.6	n.*41+2345C>G		intron_variant	Intron 5 of 7	1		ENSP00000474191.1

Frequencies

GnomAD3 genomes AF: 0.564 AC: 85628 AN: 151920 Hom.: 25221 Cov.: 32

Gnomad AFR AF: 0.716

Gnomad AMI AF: 0.314

Gnomad AMR AF: 0.526

Gnomad ASJ AF: 0.584

Gnomad EAS AF: 0.829

Gnomad SAS AF: 0.603

Gnomad FIN AF: 0.527

Gnomad MID AF: 0.579

Gnomad NFE AF: 0.465

Gnomad OTH AF: 0.540

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

GnomAD4 genome AF: 0.564 AC: 85687 AN: 152038 Hom.: 25244 Cov.: 32 AF XY: 0.570 AC XY: 42360 AN XY: 74306

African (AFR) AF: 0.716 AC: 29711 AN: 41468

American (AMR) AF: 0.525 AC: 8020 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.584 AC: 2026 AN: 3472

East Asian (EAS) AF: 0.829 AC: 4288 AN: 5172

South Asian (SAS) AF: 0.602 AC: 2901 AN: 4822

European-Finnish (FIN) AF: 0.527 AC: 5551 AN: 10538

Middle Eastern (MID) AF: 0.565 AC: 166 AN: 294

European-Non Finnish (NFE) AF: 0.465 AC: 31609 AN: 67970

Other (OTH) AF: 0.535 AC: 1129 AN: 2112

Alfa AF: 0.385 Hom.: 1080

Bravo AF: 0.569

Asia WGS AF: 0.689 AC: 2398 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.62
CADD	Benign	6.2
DANN	Benign	0.64
PhyloP100		-0.15
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs2915228; hg19: chr11-34901878;