chr19-1803583-G-T

Variant names:

• chr19-1803583-G-T
• rs7253430
• NM_138813.4:c.905-938C>A

Variant summary

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

The NM_138813.4(ATP8B3):​c.905-938C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.254 in 152,122 control chromosomes in the GnomAD database, including 5,895 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 0.25 (5895 hom., cov: 31)
• Consequence: ATP8B3 NM_138813.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.67
• Publications: 8 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.423 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_138813.4. 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
	ATP8B3	NM_138813.4	MANE Select	c.905-938C>A		intron	N/A	NP_620168.1
	ATP8B3	NM_001178002.3		c.746-938C>A		intron	N/A	NP_001171473.1
	ATP8B3	NR_047593.3		n.1371-938C>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ATP8B3	ENST00000310127.10	TSL:1 MANE Select	c.905-938C>A		intron	N/A	ENSP00000311336.6
	ATP8B3	ENST00000525591.5	TSL:1	c.746-938C>A		intron	N/A	ENSP00000437115.1
	ATP8B3	ENST00000526092.6	TSL:2	c.746-938C>A		intron	N/A	ENSP00000445204.1

Frequencies

GnomAD3 genomes AF: 0.254 AC: 38600 AN: 152004 Hom.: 5867 Cov.: 31

Gnomad AFR AF: 0.428

Gnomad AMI AF: 0.226

Gnomad AMR AF: 0.176

Gnomad ASJ AF: 0.142

Gnomad EAS AF: 0.288

Gnomad SAS AF: 0.160

Gnomad FIN AF: 0.135

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.195

Gnomad OTH AF: 0.235

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

GnomAD4 genome AF: 0.254 AC: 38685 AN: 152122 Hom.: 5895 Cov.: 31 AF XY: 0.248 AC XY: 18437 AN XY: 74396

African (AFR) AF: 0.429 AC: 17784 AN: 41482

American (AMR) AF: 0.176 AC: 2692 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.142 AC: 492 AN: 3470

East Asian (EAS) AF: 0.288 AC: 1491 AN: 5170

South Asian (SAS) AF: 0.160 AC: 773 AN: 4820

European-Finnish (FIN) AF: 0.135 AC: 1432 AN: 10598

Middle Eastern (MID) AF: 0.0884 AC: 26 AN: 294

European-Non Finnish (NFE) AF: 0.195 AC: 13274 AN: 67982

Other (OTH) AF: 0.244 AC: 515 AN: 2112

Alfa AF: 0.225 Hom.: 7538

Bravo AF: 0.263

Asia WGS AF: 0.236 AC: 823 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.027
DANN	Benign	0.34
PhyloP100		-3.7
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

Other links and lift over

dbSNP: rs7253430; hg19: chr19-1803582;