9-114351457-C-T

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
AKNA	NM_001317950.2	c.3059-436G>A		intron_variant	Intron 14 of 21	ENST00000374088.8	NP_001304879.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
AKNA	ENST00000374088.8	c.3059-436G>A		intron_variant	Intron 14 of 21	2	NM_001317950.2	ENSP00000363201.3
AKNA	ENST00000307564.8	c.3059-436G>A		intron_variant	Intron 14 of 21	1		ENSP00000303769.4
AKNA	ENST00000374075.9	c.2816-436G>A		intron_variant	Intron 12 of 19	1		ENSP00000363188.5
AKNA	ENST00000223791.7	c.1439-436G>A		intron_variant	Intron 13 of 20	2		ENSP00000223791.3

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

Gnomad4 AFR AF: 0.162

Gnomad4 AMR AF: 0.465

Gnomad4 ASJ AF: 0.584

Gnomad4 EAS AF: 0.404

Gnomad4 SAS AF: 0.558

Gnomad4 FIN AF: 0.500

Gnomad4 NFE AF: 0.523

Gnomad4 OTH AF: 0.460

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.8
DANN	Benign	0.65

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

Publications

LitVar

Other links and lift over

dbSNP: rs10739408; hg19: chr9-117113737;