5-82299265-T-C

Variant names:

• chr5-82299265-T-C
• rs2215128
• ENST00000380167.8:n.521+3721T>C

Variant summary

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

The ENST00000380167.8(ENSG00000293465):​n.521+3721T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.31 in 148,662 control chromosomes in the GnomAD database, including 8,762 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 0.31 (8762 hom., cov: 25)
• Consequence: ENSG00000293465 ENST00000380167.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.503
• Publications: 9 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=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.725 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ATP6AP1L	NR_169868.1		n.1131-4222T>C		intron	N/A
	ATP6AP1L	NR_169870.1		n.1182+3721T>C		intron	N/A
	ATP6AP1L	NR_169871.1		n.1131-4222T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000293465	ENST00000380167.8	TSL:2	n.521+3721T>C		intron	N/A
	ATP6AP1L	ENST00000643922.1		n.96+3721T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.310 AC: 46098 AN: 148568 Hom.: 8748 Cov.: 25

Gnomad AFR AF: 0.131

Gnomad AMI AF: 0.259

Gnomad AMR AF: 0.493

Gnomad ASJ AF: 0.331

Gnomad EAS AF: 0.746

Gnomad SAS AF: 0.363

Gnomad FIN AF: 0.289

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.343

Gnomad OTH AF: 0.331

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

GnomAD4 genome AF: 0.310 AC: 46123 AN: 148662 Hom.: 8762 Cov.: 25 AF XY: 0.314 AC XY: 22677 AN XY: 72328

African (AFR) AF: 0.131 AC: 5321 AN: 40542

American (AMR) AF: 0.494 AC: 7292 AN: 14756

Ashkenazi Jewish (ASJ) AF: 0.331 AC: 1144 AN: 3456

East Asian (EAS) AF: 0.745 AC: 3731 AN: 5006

South Asian (SAS) AF: 0.363 AC: 1701 AN: 4682

European-Finnish (FIN) AF: 0.289 AC: 2766 AN: 9564

Middle Eastern (MID) AF: 0.321 AC: 93 AN: 290

European-Non Finnish (NFE) AF: 0.343 AC: 23147 AN: 67402

Other (OTH) AF: 0.337 AC: 692 AN: 2054

Alfa AF: 0.340 Hom.: 18584

Bravo AF: 0.324

Asia WGS AF: 0.541 AC: 1882 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.2
DANN	Benign	0.64
PhyloP100		-0.50
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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2215128;

hg19: chr5-81595084;