17-30838916-C-G

Variant names:

• chr17-30838916-C-G
• rs9890032
• NM_024857.5:c.2076+1602C>G

Variant summary

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

The NM_024857.5(ATAD5):​c.2076+1602C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.485 in 152,096 control chromosomes in the GnomAD database, including 19,842 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 0.48 (19842 hom., cov: 33)
• Consequence: ATAD5 NM_024857.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.103
• Publications: 19 publications found

Genes affected

ATAD5 (HGNC:25752): (ATPase family AAA domain containing 5) Enables DNA clamp unloader activity. Involved in DNA clamp unloading; positive regulation of DNA replication; and positive regulation of cell cycle G2/M phase transition. Part of Elg1 RFC-like complex. Biomarker of neurilemmoma. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000265334 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.739 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_024857.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ATAD5	NM_024857.5	MANE Select	c.2076+1602C>G		intron	N/A	NP_079133.3

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ATAD5	ENST00000321990.5	TSL:1 MANE Select	c.2076+1602C>G		intron	N/A	ENSP00000313171.4
	ATAD5	ENST00000578295.5	TSL:1	n.2076+1602C>G		intron	N/A	ENSP00000463102.1
	ENSG00000265334	ENST00000580873.1	TSL:2	n.334-4287G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.484 AC: 73575 AN: 151978 Hom.: 19792 Cov.: 33

Gnomad AFR AF: 0.746

Gnomad AMI AF: 0.485

Gnomad AMR AF: 0.423

Gnomad ASJ AF: 0.329

Gnomad EAS AF: 0.228

Gnomad SAS AF: 0.413

Gnomad FIN AF: 0.375

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.390

Gnomad OTH AF: 0.440

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

GnomAD4 genome AF: 0.485 AC: 73691 AN: 152096 Hom.: 19842 Cov.: 33 AF XY: 0.479 AC XY: 35641 AN XY: 74332

African (AFR) AF: 0.746 AC: 30961 AN: 41488

American (AMR) AF: 0.422 AC: 6455 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.329 AC: 1144 AN: 3472

East Asian (EAS) AF: 0.228 AC: 1182 AN: 5178

South Asian (SAS) AF: 0.413 AC: 1993 AN: 4820

European-Finnish (FIN) AF: 0.375 AC: 3963 AN: 10556

Middle Eastern (MID) AF: 0.438 AC: 128 AN: 292

European-Non Finnish (NFE) AF: 0.390 AC: 26487 AN: 67986

Other (OTH) AF: 0.444 AC: 937 AN: 2112

Alfa AF: 0.308 Hom.: 811

Bravo AF: 0.497

Asia WGS AF: 0.369 AC: 1284 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	8.5
DANN	Benign	0.79
PhyloP100		0.10
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: rs9890032; hg19: chr17-29165934;