17-56100621-T-G

Variant names:

• chr17-56100621-T-G
• rs9894332
• ENST00000653862.1:c.462+54296T>G

Variant summary

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

The ENST00000653862.1(ANKFN1):​c.462+54296T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.573 in 151,986 control chromosomes in the GnomAD database, including 25,163 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 0.57 (25163 hom., cov: 32)
• Consequence: ANKFN1 ENST00000653862.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.362
• Publications: 5 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=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.672 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ANKFN1	XM_047435502.1	c.-193+54296T>G		intron_variant	Intron 1 of 19		XP_047291458.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ANKFN1	ENST00000653862.1	c.462+54296T>G		intron_variant	Intron 3 of 21			ENSP00000499705.1
ANKFN1	ENST00000635860.2	c.288+54296T>G		intron_variant	Intron 4 of 22	5		ENSP00000489811.2

Frequencies

GnomAD3 genomes AF: 0.573 AC: 87034 AN: 151868 Hom.: 25150 Cov.: 32

Gnomad AFR AF: 0.637

Gnomad AMI AF: 0.408

Gnomad AMR AF: 0.548

Gnomad ASJ AF: 0.425

Gnomad EAS AF: 0.691

Gnomad SAS AF: 0.551

Gnomad FIN AF: 0.576

Gnomad MID AF: 0.436

Gnomad NFE AF: 0.543

Gnomad OTH AF: 0.543

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

GnomAD4 genome AF: 0.573 AC: 87093 AN: 151986 Hom.: 25163 Cov.: 32 AF XY: 0.574 AC XY: 42608 AN XY: 74288

African (AFR) AF: 0.636 AC: 26371 AN: 41440

American (AMR) AF: 0.549 AC: 8391 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.425 AC: 1472 AN: 3466

East Asian (EAS) AF: 0.691 AC: 3553 AN: 5144

South Asian (SAS) AF: 0.550 AC: 2643 AN: 4806

European-Finnish (FIN) AF: 0.576 AC: 6099 AN: 10580

Middle Eastern (MID) AF: 0.432 AC: 126 AN: 292

European-Non Finnish (NFE) AF: 0.543 AC: 36920 AN: 67940

Other (OTH) AF: 0.542 AC: 1146 AN: 2114

Alfa AF: 0.542 Hom.: 19317

Bravo AF: 0.572

Asia WGS AF: 0.597 AC: 2079 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	5.3
DANN	Benign	0.66
PhyloP100		0.36

Splicing

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

Other links and lift over

dbSNP: rs9894332; hg19: chr17-54177982;