rs17758761

Positions:

• chr17-55977164-A-C

Variant summary

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

The ENST00000653862.1(ANKFN1):​c.208+11488A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0423 in 152,260 control chromosomes in the GnomAD database, including 166 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 0.042 (166 hom., cov: 32)
• Consequence: ANKFN1 ENST00000653862.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.01

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=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0886 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ANKFN1	ENST00000635860.2	c.34+11488A>C		intron_variant		5		ENSP00000489811	A2
ANKFN1	ENST00000653862.1	c.208+11488A>C		intron_variant				ENSP00000499705	A2

Frequencies

GnomAD3 genomes AF: 0.0423 AC: 6439 AN: 152142 Hom.: 167 Cov.: 32

Gnomad AFR AF: 0.0576

Gnomad AMI AF: 0.0274

Gnomad AMR AF: 0.0359

Gnomad ASJ AF: 0.0668

Gnomad EAS AF: 0.0646

Gnomad SAS AF: 0.0972

Gnomad FIN AF: 0.00669

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0333

Gnomad OTH AF: 0.0425

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

GnomAD4 genome AF: 0.0423 AC: 6441 AN: 152260 Hom.: 166 Cov.: 32 AF XY: 0.0433 AC XY: 3223 AN XY: 74446

Gnomad4 AFR AF: 0.0576

Gnomad4 AMR AF: 0.0359

Gnomad4 ASJ AF: 0.0668

Gnomad4 EAS AF: 0.0644

Gnomad4 SAS AF: 0.0958

Gnomad4 FIN AF: 0.00669

Gnomad4 NFE AF: 0.0333

Gnomad4 OTH AF: 0.0430

Alfa AF: 0.0389 Hom.: 128

Bravo AF: 0.0445

Asia WGS AF: 0.0850 AC: 295 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	8.8
DANN	Benign	0.75

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs17758761; hg19: chr17-54054525;