NM_001317950.2:c.3059-436G>A

Variant names:

• chr9-114351457-C-T
• rs10739408
• NM_001317950.2:c.3059-436G>A

Variant summary

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

The NM_001317950.2(AKNA):​c.3059-436G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.415 in 151,914 control chromosomes in the GnomAD database, including 15,043 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 0.42 (15043 hom., cov: 31)
• Consequence: AKNA NM_001317950.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.225
• Publications: 1 publications found

Genes affected

AKNA (HGNC:24108): (AT-hook transcription factor) Predicted to enable DNA binding activity. Involved in positive regulation of transcription by RNA polymerase II. Located in centrosome; cytosol; and nuclear lumen. [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 (SAS) allele frequency at 95% confidence interval = 0.54 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001317950.2. 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
	AKNA	NM_001317950.2	MANE Select	c.3059-436G>A		intron	N/A	NP_001304879.1
	AKNA	NM_030767.5		c.3059-436G>A		intron	N/A	NP_110394.3
	AKNA	NM_001317952.1		c.2702-436G>A		intron	N/A	NP_001304881.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AKNA	ENST00000374088.8	TSL:2 MANE Select	c.3059-436G>A		intron	N/A	ENSP00000363201.3
	AKNA	ENST00000307564.8	TSL:1	c.3059-436G>A		intron	N/A	ENSP00000303769.4
	AKNA	ENST00000374075.9	TSL:1	c.2816-436G>A		intron	N/A	ENSP00000363188.5

Frequencies

GnomAD3 genomes AF: 0.415 AC: 63062 AN: 151796 Hom.: 15048 Cov.: 31

Gnomad AFR AF: 0.162

Gnomad AMI AF: 0.581

Gnomad AMR AF: 0.466

Gnomad ASJ AF: 0.584

Gnomad EAS AF: 0.403

Gnomad SAS AF: 0.556

Gnomad FIN AF: 0.500

Gnomad MID AF: 0.566

Gnomad NFE AF: 0.523

Gnomad OTH AF: 0.464

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

GnomAD4 genome AF: 0.415 AC: 63067 AN: 151914 Hom.: 15043 Cov.: 31 AF XY: 0.416 AC XY: 30845 AN XY: 74232

African (AFR) AF: 0.162 AC: 6694 AN: 41412

American (AMR) AF: 0.465 AC: 7100 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.584 AC: 2023 AN: 3466

East Asian (EAS) AF: 0.404 AC: 2085 AN: 5158

South Asian (SAS) AF: 0.558 AC: 2679 AN: 4802

European-Finnish (FIN) AF: 0.500 AC: 5271 AN: 10538

Middle Eastern (MID) AF: 0.571 AC: 168 AN: 294

European-Non Finnish (NFE) AF: 0.523 AC: 35550 AN: 67966

Other (OTH) AF: 0.460 AC: 969 AN: 2106

Alfa AF: 0.285 Hom.: 710

Bravo AF: 0.403

Asia WGS AF: 0.425 AC: 1479 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	3.8
DANN	Benign	0.65
PhyloP100		-0.23
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs10739408; hg19: chr9-117113737;