rs1278769

Positions:

• chr13-112882313-A-G

Variant summary

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

The NM_015205.3(ATP11A):​c.*447A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.757 in 389,236 control chromosomes in the GnomAD database, including 111,953 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 0.77 (44675 hom., cov: 32)
  • Exomes 𝑓: 0.75 (67278 hom.)
• Consequence: ATP11A NM_015205.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.73

Genes affected

ATP11A (HGNC:13552): (ATPase phospholipid transporting 11A) The protein encoded by this gene is an integral membrane ATPase. The encoded protein is probably phosphorylated in its intermediate state and likely drives the transport of ions such as calcium across membranes. [provided by RefSeq, Apr 2022]

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 (AMR) allele frequency at 95% confidence interval = 0.779 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ATP11A	NM_015205.3	c.*447A>G		3_prime_UTR_variant	30/30	ENST00000375645.8	NP_056020.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ATP11A	ENST00000375645.8	c.*447A>G		3_prime_UTR_variant	30/30	5	NM_015205.3	ENSP00000364796	P1

Frequencies

GnomAD3 genomes AF: 0.766 AC: 116456 AN: 151980 Hom.: 44647 Cov.: 32

Gnomad AFR AF: 0.787

Gnomad AMI AF: 0.785

Gnomad AMR AF: 0.786

Gnomad ASJ AF: 0.696

Gnomad EAS AF: 0.685

Gnomad SAS AF: 0.725

Gnomad FIN AF: 0.767

Gnomad MID AF: 0.671

Gnomad NFE AF: 0.762

Gnomad OTH AF: 0.756

GnomAD4 exome AF: 0.751 AC: 178092 AN: 237138 Hom.: 67278 Cov.: 4 AF XY: 0.746 AC XY: 94355 AN XY: 126512

Gnomad4 AFR exome AF: 0.791

Gnomad4 AMR exome AF: 0.790

Gnomad4 ASJ exome AF: 0.694

Gnomad4 EAS exome AF: 0.672

Gnomad4 SAS exome AF: 0.716

Gnomad4 FIN exome AF: 0.758

Gnomad4 NFE exome AF: 0.763

Gnomad4 OTH exome AF: 0.754

GnomAD4 genome AF: 0.766 AC: 116533 AN: 152098 Hom.: 44675 Cov.: 32 AF XY: 0.766 AC XY: 56925 AN XY: 74340

Gnomad4 AFR AF: 0.786

Gnomad4 AMR AF: 0.787

Gnomad4 ASJ AF: 0.696

Gnomad4 EAS AF: 0.685

Gnomad4 SAS AF: 0.723

Gnomad4 FIN AF: 0.767

Gnomad4 NFE AF: 0.762

Gnomad4 OTH AF: 0.757

Alfa AF: 0.757 Hom.: 61653

Bravo AF: 0.769

Asia WGS AF: 0.774 AC: 2691 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	0.093
DANN	Benign	0.44

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: rs1278769; hg19: chr13-113536627; COSMIC: COSV52114851; COSMIC: COSV52114851;