NM_001385016.1:c.16+1457A>G

Variant names:

• chr15-52676549-T-C
• rs1991300
• NM_001385016.1:c.16+1457A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001385016.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ATOSA	NM_001385016.1	MANE Select	c.16+1457A>G		intron	N/A	NP_001371945.1	Q32MH5-1
	ATOSA	NM_001385019.1		c.16+1457A>G		intron	N/A	NP_001371948.1
	ATOSA	NM_001385013.1		c.16+1457A>G		intron	N/A	NP_001371942.1	Q32MH5-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ATOSA	ENST00000619572.5	TSL:1 MANE Select	c.16+1457A>G		intron	N/A	ENSP00000484641.1	Q32MH5-1
	ATOSA	ENST00000261844.11	TSL:1	c.16+1457A>G		intron	N/A	ENSP00000261844.7	Q32MH5-1
	ATOSA	ENST00000399202.8	TSL:1	c.-64+1457A>G		intron	N/A	ENSP00000382153.4	H0Y3Q9

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

African (AFR) AF: 0.141 AC: 5839 AN: 41532

American (AMR) AF: 0.0700 AC: 1071 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0101 AC: 35 AN: 3472

East Asian (EAS) AF: 0.273 AC: 1410 AN: 5174

South Asian (SAS) AF: 0.0396 AC: 191 AN: 4826

European-Finnish (FIN) AF: 0.0501 AC: 531 AN: 10590

Middle Eastern (MID) AF: 0.0170 AC: 5 AN: 294

European-Non Finnish (NFE) AF: 0.0384 AC: 2611 AN: 68008

Other (OTH) AF: 0.0667 AC: 141 AN: 2114

Alfa AF: 0.0470 Hom.: 160

Bravo AF: 0.0856

Asia WGS AF: 0.128 AC: 443 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	4.3
DANN	Benign	0.90
PhyloP100		-0.096
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: rs1991300; hg19: chr15-52968746;