rs1019238

Positions:

• chr17-56201354-G-A
• chr17-56201354-G-C

Variant summary

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

The NM_001370326.1(ANKFN1):​c.-70-11244G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.312 in 151,954 control chromosomes in the GnomAD database, including 8,985 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 0.31 (8985 hom., cov: 32)
• Consequence: ANKFN1 NM_001370326.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.859

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=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.495 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ANKFN1	NM_001370326.1	c.-70-11244G>A		intron_variant		ENST00000682825.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ANKFN1	ENST00000682825.1	c.-70-11244G>A		intron_variant			NM_001370326.1	A2

Frequencies

GnomAD3 genomes AF: 0.313 AC: 47487 AN: 151836 Hom.: 8996 Cov.: 32

Gnomad AFR AF: 0.0928

Gnomad AMI AF: 0.423

Gnomad AMR AF: 0.297

Gnomad ASJ AF: 0.319

Gnomad EAS AF: 0.511

Gnomad SAS AF: 0.502

Gnomad FIN AF: 0.405

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.405

Gnomad OTH AF: 0.330

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

GnomAD4 genome AF: 0.312 AC: 47458 AN: 151954 Hom.: 8985 Cov.: 32 AF XY: 0.318 AC XY: 23587 AN XY: 74274

Gnomad4 AFR AF: 0.0926

Gnomad4 AMR AF: 0.296

Gnomad4 ASJ AF: 0.319

Gnomad4 EAS AF: 0.511

Gnomad4 SAS AF: 0.501

Gnomad4 FIN AF: 0.405

Gnomad4 NFE AF: 0.405

Gnomad4 OTH AF: 0.327

Alfa AF: 0.387 Hom.: 17397

Bravo AF: 0.289

Asia WGS AF: 0.463 AC: 1613 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.40
DANN	Benign	0.43

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: rs1019238; hg19: chr17-54278715;