chr4-73104747-C-T

Position:

• chr4-73104747-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The NM_032217.5(ANKRD17):​c.4402-2200G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0272 in 140,244 control chromosomes in the GnomAD database, including 74 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 0.027 (74 hom., cov: 31)
• Consequence: ANKRD17 NM_032217.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.77

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]

LOC124900713 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BS1: Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0272 (3818/140244) while in subpopulation AFR AF= 0.0411 (1523/37040). AF 95% confidence interval is 0.0394. There are 74 homozygotes in gnomad4. There are 1853 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.
• BS2: High AC in GnomAd4 at 3818 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ANKRD17	NM_032217.5	c.4402-2200G>A		intron_variant		ENST00000358602.9	NP_115593.3
LOC124900713	XR_007058138.1	n.89+314C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ANKRD17	ENST00000358602.9	c.4402-2200G>A		intron_variant		5	NM_032217.5	ENSP00000351416

Frequencies

GnomAD3 genomes AF: 0.0272 AC: 3812 AN: 140152 Hom.: 74 Cov.: 31

Gnomad AFR AF: 0.0411

Gnomad AMI AF: 0.0324

Gnomad AMR AF: 0.0247

Gnomad ASJ AF: 0.0425

Gnomad EAS AF: 0.00236

Gnomad SAS AF: 0.0287

Gnomad FIN AF: 0.0210

Gnomad MID AF: 0.0235

Gnomad NFE AF: 0.0215

Gnomad OTH AF: 0.0286

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

GnomAD4 genome AF: 0.0272 AC: 3818 AN: 140244 Hom.: 74 Cov.: 31 AF XY: 0.0274 AC XY: 1853 AN XY: 67686

Gnomad4 AFR AF: 0.0411

Gnomad4 AMR AF: 0.0247

Gnomad4 ASJ AF: 0.0425

Gnomad4 EAS AF: 0.00237

Gnomad4 SAS AF: 0.0290

Gnomad4 FIN AF: 0.0210

Gnomad4 NFE AF: 0.0215

Gnomad4 OTH AF: 0.0283

Alfa AF: 0.0238 Hom.: 20

Bravo AF: 0.0263

Asia WGS AF: 0.0320 AC: 111 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.20
DANN	Benign	0.25

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: rs6818964; hg19: chr4-73970464;