17-56090492-T-C

Variant names:

• chr17-56090492-T-C
• rs9912513
• ENST00000653862.1:c.462+44167T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 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=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.492 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000653862.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ANKFN1	ENST00000653862.1		c.462+44167T>C		intron	N/A	ENSP00000499705.1
	ANKFN1	ENST00000635860.2	TSL:5	c.288+44167T>C		intron	N/A	ENSP00000489811.2

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

African (AFR) AF: 0.206 AC: 8469 AN: 41202

American (AMR) AF: 0.418 AC: 6326 AN: 15120

Ashkenazi Jewish (ASJ) AF: 0.427 AC: 1474 AN: 3456

East Asian (EAS) AF: 0.340 AC: 1758 AN: 5176

South Asian (SAS) AF: 0.508 AC: 2434 AN: 4788

European-Finnish (FIN) AF: 0.471 AC: 4853 AN: 10308

Middle Eastern (MID) AF: 0.348 AC: 98 AN: 282

European-Non Finnish (NFE) AF: 0.478 AC: 32298 AN: 67540

Other (OTH) AF: 0.407 AC: 852 AN: 2092

Alfa AF: 0.445 Hom.: 20360

Bravo AF: 0.373

Asia WGS AF: 0.427 AC: 1488 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.3
DANN	Benign	0.65
PhyloP100		-0.067

Splicing

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

Other links and lift over

dbSNP: rs9912513; hg19: chr17-54167853;