chr15-52676549-T-C

Position:

• chr15-52676549-T-C

Variant summary

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

The NM_001385016.1(ATOSA):​c.16+1457A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.078 in 152,218 control chromosomes in the GnomAD database, including 746 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 0.078 (746 hom., cov: 32)
• Consequence: ATOSA NM_001385016.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0960

Genes affected

ATOSA (HGNC:25609): (atos homolog A)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.261 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ATOSA	NM_001385016.1	c.16+1457A>G		intron_variant		ENST00000619572.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ATOSA	ENST00000619572.5	c.16+1457A>G		intron_variant		1	NM_001385016.1	P2

Frequencies

GnomAD3 genomes AF: 0.0780 AC: 11860 AN: 152100 Hom.: 744 Cov.: 32

Gnomad AFR AF: 0.141

Gnomad AMI AF: 0.0428

Gnomad AMR AF: 0.0700

Gnomad ASJ AF: 0.0101

Gnomad EAS AF: 0.272

Gnomad SAS AF: 0.0395

Gnomad FIN AF: 0.0501

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0384

Gnomad OTH AF: 0.0669

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

GnomAD4 genome AF: 0.0780 AC: 11873 AN: 152218 Hom.: 746 Cov.: 32 AF XY: 0.0789 AC XY: 5869 AN XY: 74426

Gnomad4 AFR AF: 0.141

Gnomad4 AMR AF: 0.0700

Gnomad4 ASJ AF: 0.0101

Gnomad4 EAS AF: 0.273

Gnomad4 SAS AF: 0.0396

Gnomad4 FIN AF: 0.0501

Gnomad4 NFE AF: 0.0384

Gnomad4 OTH AF: 0.0667

Alfa AF: 0.0458 Hom.: 128

Bravo AF: 0.0856

Asia WGS AF: 0.128 AC: 443 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	4.3
DANN	Benign	0.90

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

Publications

LitVar

Other links and lift over

dbSNP: rs1991300; hg19: chr15-52968746;