rs17758761

Variant names:

• chr17-55977164-A-C
• rs17758761
• ENST00000653862.1:c.208+11488A>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ANKFN1	ENST00000653862.1	c.208+11488A>C		intron_variant	Intron 2 of 21			ENSP00000499705.1
ANKFN1	ENST00000635860.2	c.34+11488A>C		intron_variant	Intron 3 of 22	5		ENSP00000489811.2

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

African (AFR) AF: 0.0576 AC: 2394 AN: 41538

American (AMR) AF: 0.0359 AC: 549 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0668 AC: 232 AN: 3472

East Asian (EAS) AF: 0.0644 AC: 333 AN: 5174

South Asian (SAS) AF: 0.0958 AC: 462 AN: 4822

European-Finnish (FIN) AF: 0.00669 AC: 71 AN: 10614

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.0333 AC: 2262 AN: 68016

Other (OTH) AF: 0.0430 AC: 91 AN: 2116

Alfa AF: 0.0392 Hom.: 164

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
PhyloP100		2.0

Splicing

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

Other links and lift over

dbSNP: rs17758761; hg19: chr17-54054525;