rs17820092

Variant names:

• chr17-56303538-G-A
• rs17820092
• NM_001370326.1:c.54-22683G>A

Variant summary

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

The NM_001370326.1(ANKFN1):​c.54-22683G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.11 in 152,186 control chromosomes in the GnomAD database, including 979 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 0.11 (979 hom., cov: 32)
• Consequence: ANKFN1 NM_001370326.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.518
• Publications: 1 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=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.159 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001370326.1. 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
	ANKFN1	NM_001370326.1	MANE Select	c.54-22683G>A		intron	N/A	NP_001357255.1
	ANKFN1	NM_001365758.1		c.-151-22683G>A		intron	N/A	NP_001352687.1
	ANKFN1	NM_153228.3		c.63-22683G>A		intron	N/A	NP_694960.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ANKFN1	ENST00000682825.1	MANE Select	c.54-22683G>A		intron	N/A	ENSP00000507365.1
	ANKFN1	ENST00000653862.1		c.504-22683G>A		intron	N/A	ENSP00000499705.1
	ANKFN1	ENST00000635860.2	TSL:5	c.330-22683G>A		intron	N/A	ENSP00000489811.2

Frequencies

GnomAD3 genomes AF: 0.110 AC: 16722 AN: 152068 Hom.: 968 Cov.: 32

Gnomad AFR AF: 0.161

Gnomad AMI AF: 0.0329

Gnomad AMR AF: 0.109

Gnomad ASJ AF: 0.0568

Gnomad EAS AF: 0.158

Gnomad SAS AF: 0.0852

Gnomad FIN AF: 0.0889

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0849

Gnomad OTH AF: 0.0980

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

GnomAD4 genome AF: 0.110 AC: 16763 AN: 152186 Hom.: 979 Cov.: 32 AF XY: 0.110 AC XY: 8203 AN XY: 74408

African (AFR) AF: 0.162 AC: 6720 AN: 41514

American (AMR) AF: 0.108 AC: 1657 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0568 AC: 197 AN: 3470

East Asian (EAS) AF: 0.158 AC: 817 AN: 5172

South Asian (SAS) AF: 0.0842 AC: 406 AN: 4820

European-Finnish (FIN) AF: 0.0889 AC: 942 AN: 10594

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.0849 AC: 5774 AN: 68006

Other (OTH) AF: 0.0979 AC: 207 AN: 2114

Alfa AF: 0.101 Hom.: 148

Bravo AF: 0.118

Asia WGS AF: 0.135 AC: 467 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.60
DANN	Benign	0.30
PhyloP100		-0.52
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs17820092; hg19: chr17-54380899;