5-82297200-C-A

Variant names:

• chr5-82297200-C-A
• rs226206
• ENST00000380167.8:n.521+1656C>A

Variant summary

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

The ENST00000380167.8(ENSG00000293465):​n.521+1656C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.697 in 152,064 control chromosomes in the GnomAD database, including 37,338 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 0.70 (37338 hom., cov: 32)
• Consequence: ENSG00000293465 ENST00000380167.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.21
• Publications: 16 publications found

Genes affected

ENSG00000293465 (HGNC:):

ATP6AP1L (HGNC:28091): (ATPase H+ transporting accessory protein 1 like (pseudogene)) Predicted to be involved in regulation of cellular pH. Predicted to be integral component of membrane. Predicted to be part of plasma membrane proton-transporting V-type ATPase complex. [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=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.9 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000380167.8. 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
	ATP6AP1L	NR_169868.1		n.1131-6287C>A		intron	N/A
	ATP6AP1L	NR_169870.1		n.1182+1656C>A		intron	N/A
	ATP6AP1L	NR_169871.1		n.1131-6287C>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000293465	ENST00000380167.8	TSL:2	n.521+1656C>A		intron	N/A
	ATP6AP1L	ENST00000643922.1		n.96+1656C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.697 AC: 105919 AN: 151946 Hom.: 37283 Cov.: 32

Gnomad AFR AF: 0.631

Gnomad AMI AF: 0.548

Gnomad AMR AF: 0.772

Gnomad ASJ AF: 0.638

Gnomad EAS AF: 0.922

Gnomad SAS AF: 0.835

Gnomad FIN AF: 0.681

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.701

Gnomad OTH AF: 0.699

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

GnomAD4 genome AF: 0.697 AC: 106031 AN: 152064 Hom.: 37338 Cov.: 32 AF XY: 0.701 AC XY: 52133 AN XY: 74326

African (AFR) AF: 0.632 AC: 26193 AN: 41472

American (AMR) AF: 0.773 AC: 11820 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.638 AC: 2213 AN: 3470

East Asian (EAS) AF: 0.922 AC: 4758 AN: 5162

South Asian (SAS) AF: 0.835 AC: 4022 AN: 4814

European-Finnish (FIN) AF: 0.681 AC: 7196 AN: 10560

Middle Eastern (MID) AF: 0.651 AC: 190 AN: 292

European-Non Finnish (NFE) AF: 0.701 AC: 47659 AN: 67984

Other (OTH) AF: 0.703 AC: 1482 AN: 2108

Alfa AF: 0.701 Hom.: 30568

Bravo AF: 0.700

Asia WGS AF: 0.873 AC: 3038 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.31
DANN	Benign	0.79
PhyloP100		-1.2
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: rs226206; hg19: chr5-81593019;