chr17-56213790-A-C

Position:

• chr17-56213790-A-C

Variant summary

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

The NM_001370326.1(ANKFN1):​c.12+1111A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.371 in 152,104 control chromosomes in the GnomAD database, including 12,339 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 0.37 (12339 hom., cov: 33)
• Consequence: ANKFN1 NM_001370326.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.20

Genes affected

ANKFN1 (HGNC:26766): (ankyrin repeat and fibronectin type III domain containing 1) Predicted to be involved in establishment of mitotic spindle orientation and regulation of establishment of bipolar cell polarity. Predicted to act upstream of or within behavioral fear response; equilibrioception; and locomotor rhythm. Predicted to be active in spindle. [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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.598 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ANKFN1	NM_001370326.1	c.12+1111A>C		intron_variant		ENST00000682825.1	NP_001357255.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ANKFN1	ENST00000682825.1	c.12+1111A>C		intron_variant			NM_001370326.1	ENSP00000507365	A2

Frequencies

GnomAD3 genomes AF: 0.370 AC: 56244 AN: 151986 Hom.: 12303 Cov.: 33

Gnomad AFR AF: 0.604

Gnomad AMI AF: 0.195

Gnomad AMR AF: 0.436

Gnomad ASJ AF: 0.226

Gnomad EAS AF: 0.428

Gnomad SAS AF: 0.252

Gnomad FIN AF: 0.309

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.237

Gnomad OTH AF: 0.336

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

GnomAD4 genome AF: 0.371 AC: 56357 AN: 152104 Hom.: 12339 Cov.: 33 AF XY: 0.371 AC XY: 27600 AN XY: 74350

Gnomad4 AFR AF: 0.604

Gnomad4 AMR AF: 0.437

Gnomad4 ASJ AF: 0.226

Gnomad4 EAS AF: 0.429

Gnomad4 SAS AF: 0.254

Gnomad4 FIN AF: 0.309

Gnomad4 NFE AF: 0.237

Gnomad4 OTH AF: 0.341

Alfa AF: 0.251 Hom.: 10256

Bravo AF: 0.395

Asia WGS AF: 0.354 AC: 1232 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	8.1
DANN	Benign	0.77

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: rs7209891; hg19: chr17-54291151;