rs6505045

chr17-56180997-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001370326.1(ANKFN1):c.-71+27467C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.737 in 152,122 control chromosomes in the GnomAD database, including 42,285 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 0.74 (42285 hom., cov: 32)
• Consequence: ANKFN1 NM_001370326.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.454

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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.915 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ANKFN1	NM_001370326.1	c.-71+27467C>T		intron_variant		ENST00000682825.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ANKFN1	ENST00000682825.1	c.-71+27467C>T		intron_variant			NM_001370326.1	A2

Frequencies

GnomAD3 genomes AF: 0.736 AC: 111950 AN: 152004 Hom.: 42226 Cov.: 32

Gnomad AFR AF: 0.887

Gnomad AMI AF: 0.619

Gnomad AMR AF: 0.754

Gnomad ASJ AF: 0.545

Gnomad EAS AF: 0.937

Gnomad SAS AF: 0.753

Gnomad FIN AF: 0.722

Gnomad MID AF: 0.598

Gnomad NFE AF: 0.640

Gnomad OTH AF: 0.700

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

GnomAD4 genome AF: 0.737 AC: 112072 AN: 152122 Hom.: 42285 Cov.: 32 AF XY: 0.741 AC XY: 55134 AN XY: 74372

Gnomad4 AFR AF: 0.887

Gnomad4 AMR AF: 0.754

Gnomad4 ASJ AF: 0.545

Gnomad4 EAS AF: 0.937

Gnomad4 SAS AF: 0.754

Gnomad4 FIN AF: 0.722

Gnomad4 NFE AF: 0.640

Gnomad4 OTH AF: 0.701

Alfa AF: 0.651 Hom.: 33068

Bravo AF: 0.744

Asia WGS AF: 0.829 AC: 2883 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.20
Dann	Benign	0.33

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: rs6505045; hg19: chr17-54258358;