rs1553896

Variant names:

• chr15-25869153-C-T
• rs1553896
• ENST00000557558.2:n.256+3634C>T

Variant summary

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

The ENST00000557558.2(ATP10A-DT):​n.256+3634C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.738 in 151,952 control chromosomes in the GnomAD database, including 43,081 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 0.74 (43081 hom., cov: 30)
• Consequence: ATP10A-DT ENST00000557558.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.43
• Publications: 4 publications found

Genes affected

ATP10A-DT (HGNC:55434): (ATP10A divergent transcript)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.15).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.833 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ATP10A-DT	NR_183988.1	n.639+3245C>T		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ATP10A-DT	ENST00000557558.2	n.256+3634C>T		intron_variant	Intron 1 of 1	3
ATP10A-DT	ENST00000792269.1	n.629+3245C>T		intron_variant	Intron 1 of 1
ATP10A-DT	ENST00000792270.1	n.266+3245C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.739 AC: 112169 AN: 151836 Hom.: 43079 Cov.: 30

Gnomad AFR AF: 0.510

Gnomad AMI AF: 0.770

Gnomad AMR AF: 0.791

Gnomad ASJ AF: 0.855

Gnomad EAS AF: 0.726

Gnomad SAS AF: 0.697

Gnomad FIN AF: 0.891

Gnomad MID AF: 0.829

Gnomad NFE AF: 0.839

Gnomad OTH AF: 0.766

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

GnomAD4 genome AF: 0.738 AC: 112210 AN: 151952 Hom.: 43081 Cov.: 30 AF XY: 0.741 AC XY: 55037 AN XY: 74256

African (AFR) AF: 0.510 AC: 21087 AN: 41370

American (AMR) AF: 0.791 AC: 12080 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.855 AC: 2967 AN: 3472

East Asian (EAS) AF: 0.725 AC: 3718 AN: 5126

South Asian (SAS) AF: 0.696 AC: 3350 AN: 4816

European-Finnish (FIN) AF: 0.891 AC: 9438 AN: 10594

Middle Eastern (MID) AF: 0.820 AC: 241 AN: 294

European-Non Finnish (NFE) AF: 0.839 AC: 57014 AN: 67990

Other (OTH) AF: 0.765 AC: 1613 AN: 2108

Alfa AF: 0.804 Hom.: 90905

Bravo AF: 0.725

Asia WGS AF: 0.661 AC: 2299 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.0070
DANN	Benign	0.72
PhyloP100		-3.4

Splicing

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

Other links and lift over

dbSNP: rs1553896; hg19: chr15-26114300;