17-56125999-G-T

Variant names:

• chr17-56125999-G-T
• rs8065311
• ENST00000653862.1:c.462+79674G>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000653862.1(ANKFN1):​c.462+79674G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.309 in 151,972 control chromosomes in the GnomAD database, including 8,953 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 0.31 (8953 hom., cov: 32)
• Consequence: ANKFN1 ENST00000653862.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.432
• Publications: 10 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=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.515 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ANKFN1	ENST00000653862.1		c.462+79674G>T		intron	N/A	ENSP00000499705.1
	ANKFN1	ENST00000635860.2	TSL:5	c.288+79674G>T		intron	N/A	ENSP00000489811.2
	ANKFN1	ENST00000575594.1	TSL:3	n.89+14953G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.309 AC: 46931 AN: 151854 Hom.: 8965 Cov.: 32

Gnomad AFR AF: 0.0834

Gnomad AMI AF: 0.365

Gnomad AMR AF: 0.265

Gnomad ASJ AF: 0.308

Gnomad EAS AF: 0.531

Gnomad SAS AF: 0.493

Gnomad FIN AF: 0.423

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.407

Gnomad OTH AF: 0.326

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

GnomAD4 genome AF: 0.309 AC: 46900 AN: 151972 Hom.: 8953 Cov.: 32 AF XY: 0.313 AC XY: 23265 AN XY: 74256

African (AFR) AF: 0.0832 AC: 3452 AN: 41494

American (AMR) AF: 0.265 AC: 4051 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.308 AC: 1069 AN: 3468

East Asian (EAS) AF: 0.531 AC: 2717 AN: 5112

South Asian (SAS) AF: 0.491 AC: 2363 AN: 4810

European-Finnish (FIN) AF: 0.423 AC: 4463 AN: 10544

Middle Eastern (MID) AF: 0.306 AC: 90 AN: 294

European-Non Finnish (NFE) AF: 0.407 AC: 27681 AN: 67946

Other (OTH) AF: 0.324 AC: 682 AN: 2108

Alfa AF: 0.364 Hom.: 24633

Bravo AF: 0.282

Asia WGS AF: 0.464 AC: 1616 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	13
DANN	Benign	0.63
PhyloP100		0.43

Splicing

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

Other links and lift over

dbSNP: rs8065311; hg19: chr17-54203360;