17-56303538-G-A

Position:

• chr17-56303538-G-A

Variant summary

Our verdict is Benign. Variant got -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

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=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.159 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ANKFN1	NM_001370326.1	c.54-22683G>A		intron_variant		ENST00000682825.1	NP_001357255.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ANKFN1	ENST00000682825.1	c.54-22683G>A		intron_variant			NM_001370326.1	ENSP00000507365.1

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

Gnomad4 AFR AF: 0.162

Gnomad4 AMR AF: 0.108

Gnomad4 ASJ AF: 0.0568

Gnomad4 EAS AF: 0.158

Gnomad4 SAS AF: 0.0842

Gnomad4 FIN AF: 0.0889

Gnomad4 NFE AF: 0.0849

Gnomad4 OTH AF: 0.0979

Alfa AF: 0.0997 Hom.: 140

Bravo AF: 0.118

Asia WGS AF: 0.135 AC: 467 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.60
DANN	Benign	0.30

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

Publications

LitVar

Other links and lift over

dbSNP: rs17820092; hg19: chr17-54380899;