rs1553896

chr15-25869153-C-T

Variant summary

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

The NR_183988.1(ATP10A-DT):n.639+3245C>T variant causes a intron, non coding transcript 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 NR_183988.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.43

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
ATP10A-DT	NR_183988.1	n.639+3245C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ATP10A-DT	ENST00000557558.1	n.225+3634C>T		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR AF: 0.510

Gnomad4 AMR AF: 0.791

Gnomad4 ASJ AF: 0.855

Gnomad4 EAS AF: 0.725

Gnomad4 SAS AF: 0.696

Gnomad4 FIN AF: 0.891

Gnomad4 NFE AF: 0.839

Gnomad4 OTH AF: 0.765

Alfa AF: 0.817 Hom.: 66968

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1553896; hg19: chr15-26114300;