chr17-56040131-G-A

Variant names:

• chr17-56040131-G-A
• rs9303380
• ENST00000653862.1:c.209-5941G>A

Variant summary

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

The ENST00000653862.1(ANKFN1):​c.209-5941G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.117 in 152,042 control chromosomes in the GnomAD database, including 1,921 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 0.12 (1921 hom., cov: 32)
• Consequence: ANKFN1 ENST00000653862.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.189
• 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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.281 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ANKFN1	ENST00000653862.1	c.209-5941G>A		intron_variant	Intron 2 of 21			ENSP00000499705.1
ANKFN1	ENST00000635860.2	c.35-5941G>A		intron_variant	Intron 3 of 22	5		ENSP00000489811.2

Frequencies

GnomAD3 genomes AF: 0.117 AC: 17786 AN: 151924 Hom.: 1907 Cov.: 32

Gnomad AFR AF: 0.285

Gnomad AMI AF: 0.0658

Gnomad AMR AF: 0.0678

Gnomad ASJ AF: 0.0833

Gnomad EAS AF: 0.0629

Gnomad SAS AF: 0.0474

Gnomad FIN AF: 0.0338

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.0509

Gnomad OTH AF: 0.100

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

GnomAD4 genome AF: 0.117 AC: 17830 AN: 152042 Hom.: 1921 Cov.: 32 AF XY: 0.114 AC XY: 8481 AN XY: 74326

African (AFR) AF: 0.286 AC: 11833 AN: 41440

American (AMR) AF: 0.0677 AC: 1035 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0833 AC: 289 AN: 3468

East Asian (EAS) AF: 0.0626 AC: 324 AN: 5172

South Asian (SAS) AF: 0.0475 AC: 228 AN: 4802

European-Finnish (FIN) AF: 0.0338 AC: 358 AN: 10590

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.0509 AC: 3460 AN: 67966

Other (OTH) AF: 0.0991 AC: 209 AN: 2110

Alfa AF: 0.0712 Hom.: 1132

Bravo AF: 0.127

Asia WGS AF: 0.0770 AC: 267 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.4
DANN	Benign	0.28
PhyloP100		0.19

Splicing

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

Other links and lift over

dbSNP: rs9303380; hg19: chr17-54117492;