17-30837005-C-A

Variant names:

• chr17-30837005-C-A
• rs3764419
• NM_024857.5:c.1968-201C>A

Variant summary

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

The NM_024857.5(ATAD5):​c.1968-201C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.484 in 151,904 control chromosomes in the GnomAD database, including 19,789 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 (19789 hom., cov: 31)
• Consequence: ATAD5 NM_024857.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.62
• Publications: 49 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=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.739 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ATAD5	NM_024857.5	c.1968-201C>A		intron_variant	Intron 2 of 22	ENST00000321990.5	NP_079133.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ATAD5	ENST00000321990.5	c.1968-201C>A		intron_variant	Intron 2 of 22	1	NM_024857.5	ENSP00000313171.4
ATAD5	ENST00000578295.5	n.1968-201C>A		intron_variant	Intron 2 of 14	1		ENSP00000463102.1
ENSG00000265334	ENST00000580873.1	n.334-2376G>T		intron_variant	Intron 1 of 1	2
ATAD5	ENST00000585133.1	n.841-201C>A		intron_variant	Intron 1 of 12	2

Frequencies

GnomAD3 genomes AF: 0.484 AC: 73425 AN: 151786 Hom.: 19739 Cov.: 31

Gnomad AFR AF: 0.746

Gnomad AMI AF: 0.486

Gnomad AMR AF: 0.422

Gnomad ASJ AF: 0.329

Gnomad EAS AF: 0.227

Gnomad SAS AF: 0.412

Gnomad FIN AF: 0.375

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.389

Gnomad OTH AF: 0.440

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

GnomAD4 genome AF: 0.484 AC: 73541 AN: 151904 Hom.: 19789 Cov.: 31 AF XY: 0.479 AC XY: 35546 AN XY: 74232

African (AFR) AF: 0.746 AC: 30908 AN: 41424

American (AMR) AF: 0.421 AC: 6423 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.329 AC: 1142 AN: 3470

East Asian (EAS) AF: 0.227 AC: 1174 AN: 5166

South Asian (SAS) AF: 0.412 AC: 1983 AN: 4810

European-Finnish (FIN) AF: 0.375 AC: 3956 AN: 10544

Middle Eastern (MID) AF: 0.432 AC: 127 AN: 294

European-Non Finnish (NFE) AF: 0.389 AC: 26449 AN: 67926

Other (OTH) AF: 0.444 AC: 936 AN: 2110

Alfa AF: 0.411 Hom.: 53327

Bravo AF: 0.497

Asia WGS AF: 0.369 AC: 1284 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.14
DANN	Benign	0.40
PhyloP100		-2.6
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: rs3764419; hg19: chr17-29164023;