rs13119179

Variant names:

• chr4-73178113-A-G
• rs13119179
• NM_032217.5:c.394-580T>C

Variant summary

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

The NM_032217.5(ANKRD17):​c.394-580T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.13 in 152,196 control chromosomes in the GnomAD database, including 1,714 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 0.13 (1714 hom., cov: 32)
• Consequence: ANKRD17 NM_032217.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.727
• Publications: 4 publications found

Genes affected

ANKRD17 (HGNC:23575): (ankyrin repeat domain 17) The protein encoded by this gene belongs to the family of ankyrin repeat-containing proteins, and contains two distinct arrays of ankyrin repeats in its amino-terminal region, one with 15 ankyrin repeats, and the other with 10 ankyrin repeats. It also contains a nuclear export signal, nuclear localization signal, and a cyclin-binding RXL motif. Localization of this protein to the nucleus has been shown experimentally, and interactions between this protein and cyclin-dependent kinase 2 have been observed. It has been suggested that this protein plays a role in both DNA replication and in both anti-viral and anti-bacterial innate immune pathways. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Dec 2015]

ANKRD17 Gene-Disease associations (from GenCC):

• Chopra-Amiel-Gordon syndrome

  Inheritance: AD Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae), G2P
• syndromic intellectual disability

  Inheritance: AD Classification: STRONG Submitted by: ClinGen

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.264 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_032217.5. 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
	ANKRD17	NM_032217.5	MANE Select	c.394-580T>C		intron	N/A	NP_115593.3
	ANKRD17	NM_015574.2		c.394-580T>C		intron	N/A	NP_056389.1
	ANKRD17	NM_001286771.3		c.55-580T>C		intron	N/A	NP_001273700.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ANKRD17	ENST00000358602.9	TSL:5 MANE Select	c.394-580T>C		intron	N/A	ENSP00000351416.4
	ANKRD17	ENST00000509867.6	TSL:1	c.55-580T>C		intron	N/A	ENSP00000427151.2
	ANKRD17	ENST00000558247.5	TSL:1	c.46-580T>C		intron	N/A	ENSP00000453434.1

Frequencies

GnomAD3 genomes AF: 0.130 AC: 19730 AN: 152078 Hom.: 1716 Cov.: 32

Gnomad AFR AF: 0.0379

Gnomad AMI AF: 0.251

Gnomad AMR AF: 0.211

Gnomad ASJ AF: 0.161

Gnomad EAS AF: 0.276

Gnomad SAS AF: 0.224

Gnomad FIN AF: 0.0722

Gnomad MID AF: 0.239

Gnomad NFE AF: 0.154

Gnomad OTH AF: 0.158

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

GnomAD4 genome AF: 0.130 AC: 19724 AN: 152196 Hom.: 1714 Cov.: 32 AF XY: 0.129 AC XY: 9618 AN XY: 74430

African (AFR) AF: 0.0377 AC: 1568 AN: 41564

American (AMR) AF: 0.211 AC: 3215 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.161 AC: 557 AN: 3470

East Asian (EAS) AF: 0.276 AC: 1431 AN: 5184

South Asian (SAS) AF: 0.225 AC: 1084 AN: 4822

European-Finnish (FIN) AF: 0.0722 AC: 765 AN: 10598

Middle Eastern (MID) AF: 0.243 AC: 71 AN: 292

European-Non Finnish (NFE) AF: 0.154 AC: 10472 AN: 67978

Other (OTH) AF: 0.157 AC: 332 AN: 2108

Alfa AF: 0.141 Hom.: 445

Bravo AF: 0.135

Asia WGS AF: 0.265 AC: 922 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	7.8
DANN	Benign	0.65
PhyloP100		0.73
Mutation Taster		=99/1	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: rs13119179; hg19: chr4-74043830;