rs6505045

Variant names:

• chr17-56180997-C-T
• rs6505045
• NM_001370326.1:c.-71+27467C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.915 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001370326.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ANKFN1	NM_001370326.1	MANE Select	c.-71+27467C>T		intron	N/A	NP_001357255.1	Q8N957-1
	ANKFN1	NM_001365758.1		c.-260-3752C>T		intron	N/A	NP_001352687.1
	ANKFN1	NM_153228.3		c.21+27467C>T		intron	N/A	NP_694960.2	Q8N957-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ANKFN1	ENST00000682825.1	MANE Select	c.-71+27467C>T		intron	N/A	ENSP00000507365.1	Q8N957-1
	ANKFN1	ENST00000653862.1		c.463-46920C>T		intron	N/A	ENSP00000499705.1	A0A590UK59
	ANKFN1	ENST00000635860.2	TSL:5	c.289-46920C>T		intron	N/A	ENSP00000489811.2	A0A1B0GTR8

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

African (AFR) AF: 0.887 AC: 36810 AN: 41516

American (AMR) AF: 0.754 AC: 11517 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.545 AC: 1891 AN: 3468

East Asian (EAS) AF: 0.937 AC: 4856 AN: 5182

South Asian (SAS) AF: 0.754 AC: 3641 AN: 4828

European-Finnish (FIN) AF: 0.722 AC: 7637 AN: 10572

Middle Eastern (MID) AF: 0.595 AC: 175 AN: 294

European-Non Finnish (NFE) AF: 0.640 AC: 43499 AN: 67966

Other (OTH) AF: 0.701 AC: 1484 AN: 2116

Alfa AF: 0.664 Hom.: 44445

Bravo AF: 0.744

Asia WGS AF: 0.829 AC: 2883 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.20
DANN	Benign	0.33
PhyloP100		-0.45
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs6505045; hg19: chr17-54258358;