rs2060070

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.05
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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
ANKFN1XM_047435502.1 linkc.-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
ANKFN1ENST00000653862.1 linkc.462+287G>A intron_variant Intron 3 of 21 ENSP00000499705.1 A0A590UK59
ANKFN1ENST00000635860.2 linkc.288+287G>A intron_variant Intron 4 of 22 5 ENSP00000489811.2 A0A1B0GTR8

Frequencies

GnomAD3 genomes
AF:
0.379
AC:
57526
AN:
151870
Hom.:
14026
Cov.:
32
show subpopulations
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
show subpopulations
Gnomad4 AFR
AF:
0.705
Gnomad4 AMR
AF:
0.224
Gnomad4 ASJ
AF:
0.226
Gnomad4 EAS
AF:
0.343
Gnomad4 SAS
AF:
0.311
Gnomad4 FIN
AF:
0.273
Gnomad4 NFE
AF:
0.249
Gnomad4 OTH
AF:
0.348
Alfa
AF:
0.295
Hom.:
4164
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

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs2060070; hg19: chr17-54123973; API