rs1923260

Positions:

• chr10-87763925-T-C
• chr10-87763925-T-G

Variant summary

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

The NM_001321967.2(ATAD1):​c.831+3748A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.294 in 151,946 control chromosomes in the GnomAD database, including 6,762 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 0.29 (6762 hom., cov: 31)
• Consequence: ATAD1 NM_001321967.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.118

Genes affected

ATAD1 (HGNC:25903): (ATPase family AAA domain containing 1) Predicted to enable ATP binding activity and transmembrane protein dislocase activity. Involved in extraction of mislocalized protein from mitochondrial outer membrane. Located in mitochondrial outer membrane and peroxisomal membrane. Implicated in hyperekplexia 4. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.306 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ATAD1	NM_001321967.2	c.831+3748A>G		intron_variant		ENST00000680024.1	NP_001308896.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ATAD1	ENST00000680024.1	c.831+3748A>G		intron_variant			NM_001321967.2	ENSP00000506333	P1

Frequencies

GnomAD3 genomes AF: 0.294 AC: 44578 AN: 151828 Hom.: 6751 Cov.: 31

Gnomad AFR AF: 0.293

Gnomad AMI AF: 0.302

Gnomad AMR AF: 0.270

Gnomad ASJ AF: 0.284

Gnomad EAS AF: 0.157

Gnomad SAS AF: 0.247

Gnomad FIN AF: 0.317

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.310

Gnomad OTH AF: 0.286

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

GnomAD4 genome AF: 0.294 AC: 44607 AN: 151946 Hom.: 6762 Cov.: 31 AF XY: 0.292 AC XY: 21678 AN XY: 74254

Gnomad4 AFR AF: 0.293

Gnomad4 AMR AF: 0.269

Gnomad4 ASJ AF: 0.284

Gnomad4 EAS AF: 0.157

Gnomad4 SAS AF: 0.245

Gnomad4 FIN AF: 0.317

Gnomad4 NFE AF: 0.310

Gnomad4 OTH AF: 0.294

Alfa AF: 0.304 Hom.: 884

Bravo AF: 0.290

Asia WGS AF: 0.236 AC: 819 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.7
DANN	Benign	0.43

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: rs1923260; hg19: chr10-89523682;