rs370415303

Variant names:

• chr19-1783243-C-A
• NM_138813.4:c.3688G>T

Your query was ambiguous. Multiple possible variants found:

• chr19-1783243-C-A
• chr19-1783243-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_138813.4(ATP8B3):​c.3688G>T​(p.Glu1230*) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000686 in 1,457,888 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 31)
  • Exomes 𝑓: 6.9e-7 (0 hom.)
• Consequence: ATP8B3 NM_138813.4 stop_gained
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0190

Genes affected

ATP8B3 (HGNC:13535): (ATPase phospholipid transporting 8B3) The protein encoded by this gene belongs to the family of P-type cation transport ATPases, and to the subfamily of aminophospholipid-transporting ATPases. The aminophospholipid translocases transport phosphatidylserine and phosphatidylethanolamine from one side of a bilayer to the other. This gene encodes member 3 of phospholipid-transporting ATPase 8B; other members of this protein family are located on chromosomes 1, 15 and 18. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Apr 2012]

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ATP8B3	NM_138813.4	c.3688G>T	p.Glu1230*	stop_gained	Exon 29 of 29	ENST00000310127.10	NP_620168.1
ATP8B3	NM_001178002.3	c.3577G>T	p.Glu1193*	stop_gained	Exon 29 of 29		NP_001171473.1
ATP8B3	NR_047593.3	n.4071G>T		non_coding_transcript_exon_variant	Exon 29 of 29

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ATP8B3	ENST00000310127.10	c.3688G>T	p.Glu1230*	stop_gained	Exon 29 of 29	1	NM_138813.4	ENSP00000311336.6
ATP8B3	ENST00000525591.5	c.3577G>T	p.Glu1193*	stop_gained	Exon 29 of 29	1		ENSP00000437115.1
ATP8B3	ENST00000531925.5	n.*3571G>T		non_coding_transcript_exon_variant	Exon 29 of 29	2		ENSP00000444334.1
ATP8B3	ENST00000531925.5	n.*3571G>T		3_prime_UTR_variant	Exon 29 of 29	2		ENSP00000444334.1

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome AF: 6.86e-7 AC: 1 AN: 1457888 Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1 AN XY: 724932

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.0000227

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Pathogenic	0.63	D
BayesDel_noAF	Pathogenic	0.28
CADD	Pathogenic	36
DANN	Uncertain	0.98
Eigen	Benign	-0.0043
Eigen_PC	Benign	-0.36
FATHMM_MKL	Benign	0.30	N
Vest4		0.089
GERP RS		1.5

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.070		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr19-1783242;