rs9912513

chr17-56090492-T-C

Variant summary

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

The ENST00000653862.1(ANKFN1):c.462+44167T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.39 in 150,876 control chromosomes in the GnomAD database, including 13,699 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 0.39 (13699 hom., cov: 31)
• Consequence: ANKFN1 ENST00000653862.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0670

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=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.492 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ANKFN1	XM_047435502.1	c.-193+44167T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ANKFN1	ENST00000635860.2	c.288+44167T>C		intron_variant		5		A2
ANKFN1	ENST00000653862.1	c.462+44167T>C		intron_variant				A2

Frequencies

GnomAD3 genomes AF: 0.391 AC: 58895 AN: 150758 Hom.: 13692 Cov.: 31

Gnomad AFR AF: 0.206

Gnomad AMI AF: 0.374

Gnomad AMR AF: 0.418

Gnomad ASJ AF: 0.427

Gnomad EAS AF: 0.340

Gnomad SAS AF: 0.509

Gnomad FIN AF: 0.471

Gnomad MID AF: 0.355

Gnomad NFE AF: 0.478

Gnomad OTH AF: 0.407

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

GnomAD4 genome AF: 0.390 AC: 58903 AN: 150876 Hom.: 13699 Cov.: 31 AF XY: 0.392 AC XY: 28828 AN XY: 73606

Gnomad4 AFR AF: 0.206

Gnomad4 AMR AF: 0.418

Gnomad4 ASJ AF: 0.427

Gnomad4 EAS AF: 0.340

Gnomad4 SAS AF: 0.508

Gnomad4 FIN AF: 0.471

Gnomad4 NFE AF: 0.478

Gnomad4 OTH AF: 0.407

Alfa AF: 0.453 Hom.: 16494

Bravo AF: 0.373

Asia WGS AF: 0.427 AC: 1488 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	1.3
Dann	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9912513; hg19: chr17-54167853;