chr13-112882313-A-T

Variant names:

• chr13-112882313-A-T
• rs1278769
• ENST00000471555.5:n.*928A>T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000471555.5(ATP11A):​n.*928A>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000421 in 237,490 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 32)
  • Exomes 𝑓: 0.0000042 (0 hom.)
• Consequence: ATP11A ENST00000471555.5 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.73
• Publications: 0 publications found

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]

ATP11A Gene-Disease associations (from GenCC):

• auditory neuropathy, autosomal dominant 2

  Inheritance: AD Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae)
• complex neurodevelopmental disorder

  Inheritance: AD Classification: MODERATE Submitted by: Ambry Genetics
• hearing loss, autosomal dominant 84

  Inheritance: AD Classification: MODERATE Submitted by: Ambry Genetics
• leukodystrophy, hypomyelinating, 24

  Inheritance: AD Classification: LIMITED Submitted by: Ambry Genetics

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000471555.5. 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
	ATP11A	NM_015205.3	MANE Select	c.*447A>T		3_prime_UTR	Exon 30 of 30	NP_056020.2
	ATP11A	NM_001405661.1		c.*249A>T		3_prime_UTR	Exon 29 of 29	NP_001392590.1
	ATP11A	NM_032189.4		c.*249A>T		3_prime_UTR	Exon 29 of 29	NP_115565.3

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ATP11A	ENST00000471555.5	TSL:1	n.*928A>T		non_coding_transcript_exon	Exon 13 of 13	ENSP00000420696.1
	ATP11A	ENST00000375645.8	TSL:5 MANE Select	c.*447A>T		3_prime_UTR	Exon 30 of 30	ENSP00000364796.3
	ATP11A	ENST00000471555.5	TSL:1	n.*928A>T		3_prime_UTR	Exon 13 of 13	ENSP00000420696.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000421 AC: 1 AN: 237490 Hom.: 0 Cov.: 4 AF XY: 0.00000789 AC XY: 1 AN XY: 126702

African (AFR) AF: 0.00 AC: 0 AN: 6222

American (AMR) AF: 0.00 AC: 0 AN: 10610

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 4998

East Asian (EAS) AF: 0.00 AC: 0 AN: 8488

South Asian (SAS) AF: 0.0000240 AC: 1 AN: 41586

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 9232

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 754

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 144540

Other (OTH) AF: 0.00 AC: 0 AN: 11060

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.077
DANN	Benign	0.55
PhyloP100		-2.7

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: rs1278769; hg19: chr13-113536627;