rs2986425

Variant names:

• chr11-34894209-A-G
• rs2986425
• NM_015957.4:c.158+801T>C

Your query was ambiguous. Multiple possible variants found:

• chr11-34894209-A-G
• chr11-34894209-A-T

Variant summary

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

The NM_015957.4(APIP):​c.158+801T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.373 in 151,878 control chromosomes in the GnomAD database, including 10,940 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 0.37 (10940 hom., cov: 31)
• Consequence: APIP NM_015957.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.438
• Publications: 5 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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.722 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_015957.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	APIP	NM_015957.4	MANE Select	c.158+801T>C		intron	N/A	NP_057041.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	APIP	ENST00000395787.4	TSL:1 MANE Select	c.158+801T>C		intron	N/A	ENSP00000379133.3
	APIP	ENST00000527830.1	TSL:2	n.125-3657T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.373 AC: 56602 AN: 151760 Hom.: 10943 Cov.: 31

Gnomad AFR AF: 0.321

Gnomad AMI AF: 0.279

Gnomad AMR AF: 0.414

Gnomad ASJ AF: 0.436

Gnomad EAS AF: 0.742

Gnomad SAS AF: 0.488

Gnomad FIN AF: 0.409

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.351

Gnomad OTH AF: 0.363

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

GnomAD4 genome AF: 0.373 AC: 56613 AN: 151878 Hom.: 10940 Cov.: 31 AF XY: 0.382 AC XY: 28362 AN XY: 74210

African (AFR) AF: 0.322 AC: 13321 AN: 41418

American (AMR) AF: 0.413 AC: 6311 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.436 AC: 1511 AN: 3466

East Asian (EAS) AF: 0.742 AC: 3833 AN: 5168

South Asian (SAS) AF: 0.487 AC: 2346 AN: 4820

European-Finnish (FIN) AF: 0.409 AC: 4297 AN: 10498

Middle Eastern (MID) AF: 0.442 AC: 129 AN: 292

European-Non Finnish (NFE) AF: 0.351 AC: 23854 AN: 67928

Other (OTH) AF: 0.359 AC: 757 AN: 2110

Alfa AF: 0.365 Hom.: 1824

Bravo AF: 0.368

Asia WGS AF: 0.594 AC: 2067 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.3
DANN	Benign	0.49
PhyloP100		-0.44
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: rs2986425; hg19: chr11-34915756;