rs226206

Positions:

• chr5-82297200-C-A
• chr5-82297200-C-G
• chr5-82297200-C-T

Variant summary

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

The NR_172122.1(ATP6AP1L):​n.1333+1656C>A 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 0.697 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: ATP6AP1L NR_172122.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.21

Genes affected

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ATP6AP1L	NR_172122.1	n.1333+1656C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ATP6AP1L	ENST00000643922.1	n.96+1656C>A		intron_variant, non_coding_transcript_variant
	ENST00000380167.8	n.521+1656C>A		intron_variant, non_coding_transcript_variant		2

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

Gnomad4 AFR AF: 0.632

Gnomad4 AMR AF: 0.773

Gnomad4 ASJ AF: 0.638

Gnomad4 EAS AF: 0.922

Gnomad4 SAS AF: 0.835

Gnomad4 FIN AF: 0.681

Gnomad4 NFE AF: 0.701

Gnomad4 OTH AF: 0.703

Alfa AF: 0.701 Hom.: 21135

Bravo AF: 0.700

Asia WGS AF: 0.873 AC: 3038 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.31
DANN	Benign	0.79

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

Publications

LitVar

Other links and lift over

dbSNP: rs226206; hg19: chr5-81593019;