17-56046612-G-A

Variant names:

• chr17-56046612-G-A
• rs2060070
• ENST00000653862.1:c.462+287G>A

Variant summary

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

The ENST00000653862.1(ANKFN1):​c.462+287G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.379 in 151,988 control chromosomes in the GnomAD database, including 14,068 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 0.38 (14068 hom., cov: 32)
• Consequence: ANKFN1 ENST00000653862.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.05
• Publications: 2 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=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.698 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ANKFN1	XM_047435502.1	c.-193+287G>A		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+287G>A		intron_variant	Intron 3 of 21			ENSP00000499705.1
ANKFN1	ENST00000635860.2	c.288+287G>A		intron_variant	Intron 4 of 22	5		ENSP00000489811.2

Frequencies

GnomAD3 genomes AF: 0.379 AC: 57526 AN: 151870 Hom.: 14026 Cov.: 32

Gnomad AFR AF: 0.705

Gnomad AMI AF: 0.316

Gnomad AMR AF: 0.225

Gnomad ASJ AF: 0.226

Gnomad EAS AF: 0.343

Gnomad SAS AF: 0.310

Gnomad FIN AF: 0.273

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.249

Gnomad OTH AF: 0.340

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

GnomAD4 genome AF: 0.379 AC: 57620 AN: 151988 Hom.: 14068 Cov.: 32 AF XY: 0.376 AC XY: 27953 AN XY: 74304

African (AFR) AF: 0.705 AC: 29210 AN: 41436

American (AMR) AF: 0.224 AC: 3428 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.226 AC: 783 AN: 3470

East Asian (EAS) AF: 0.343 AC: 1774 AN: 5176

South Asian (SAS) AF: 0.311 AC: 1494 AN: 4804

European-Finnish (FIN) AF: 0.273 AC: 2883 AN: 10564

Middle Eastern (MID) AF: 0.279 AC: 82 AN: 294

European-Non Finnish (NFE) AF: 0.249 AC: 16942 AN: 67940

Other (OTH) AF: 0.348 AC: 736 AN: 2114

Alfa AF: 0.307 Hom.: 18269

Bravo AF: 0.391

Asia WGS AF: 0.351 AC: 1220 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	9.7
DANN	Benign	0.65
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs2060070; hg19: chr17-54123973;