chr17-56494052-T-C

Variant names:

• chr17-56494052-T-C
• rs972872
• NM_001370326.1:c.2427+1699T>C

Variant summary

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

The NM_001370326.1(ANKFN1):​c.2427+1699T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.546 in 152,096 control chromosomes in the GnomAD database, including 25,579 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 0.55 (25579 hom., cov: 33)
• Consequence: ANKFN1 NM_001370326.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.329
• Publications: 3 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 (EAS) allele frequency at 95% confidence interval = 0.864 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ANKFN1	NM_001370326.1	MANE Select	c.2427+1699T>C		intron	N/A	NP_001357255.1
	ANKFN1	NM_001365758.1		c.2223+1699T>C		intron	N/A	NP_001352687.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ANKFN1	ENST00000682825.1	MANE Select	c.2427+1699T>C		intron	N/A	ENSP00000507365.1
	ANKFN1	ENST00000653862.1		c.2877+1699T>C		intron	N/A	ENSP00000499705.1
	ANKFN1	ENST00000635860.2	TSL:5	c.2703+1699T>C		intron	N/A	ENSP00000489811.2

Frequencies

GnomAD3 genomes AF: 0.546 AC: 82967 AN: 151978 Hom.: 25584 Cov.: 33

Gnomad AFR AF: 0.247

Gnomad AMI AF: 0.630

Gnomad AMR AF: 0.693

Gnomad ASJ AF: 0.595

Gnomad EAS AF: 0.886

Gnomad SAS AF: 0.642

Gnomad FIN AF: 0.653

Gnomad MID AF: 0.617

Gnomad NFE AF: 0.640

Gnomad OTH AF: 0.580

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

GnomAD4 genome AF: 0.546 AC: 82971 AN: 152096 Hom.: 25579 Cov.: 33 AF XY: 0.554 AC XY: 41230 AN XY: 74358

African (AFR) AF: 0.247 AC: 10266 AN: 41502

American (AMR) AF: 0.694 AC: 10595 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.595 AC: 2066 AN: 3472

East Asian (EAS) AF: 0.886 AC: 4576 AN: 5166

South Asian (SAS) AF: 0.642 AC: 3098 AN: 4828

European-Finnish (FIN) AF: 0.653 AC: 6909 AN: 10580

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

European-Non Finnish (NFE) AF: 0.640 AC: 43500 AN: 67968

Other (OTH) AF: 0.575 AC: 1213 AN: 2110

Alfa AF: 0.618 Hom.: 17382

Bravo AF: 0.538

Asia WGS AF: 0.704 AC: 2447 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.1
DANN	Benign	0.53
PhyloP100		0.33
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs972872; hg19: chr17-54571413;