5-82299265-T-C

Position:

• chr5-82299265-T-C

Variant summary

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

The ENST00000380167.8(ATP6AP1L):​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: ATP6AP1L ENST00000380167.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.503

Genes affected

ATP6AP1L (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ATP6AP1L	NR_169868.1	n.1131-4222T>C		intron_variant
ATP6AP1L	NR_169870.1	n.1182+3721T>C		intron_variant
ATP6AP1L	NR_169871.1	n.1131-4222T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ATP6AP1L	ENST00000380167.8	n.521+3721T>C		intron_variant		2
ATP6AP1L	ENST00000643922.1	n.96+3721T>C		intron_variant

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

Gnomad4 AFR AF: 0.131

Gnomad4 AMR AF: 0.494

Gnomad4 ASJ AF: 0.331

Gnomad4 EAS AF: 0.745

Gnomad4 SAS AF: 0.363

Gnomad4 FIN AF: 0.289

Gnomad4 NFE AF: 0.343

Gnomad4 OTH AF: 0.337

Alfa AF: 0.341 Hom.: 13519

Bravo AF: 0.324

Asia WGS AF: 0.541 AC: 1882 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

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: rs2215128; hg19: chr5-81595084;