rs12090453

chr1-108873603-T-Cchr1-108873603-T-G

Variant summary

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

The ENST00000357393.6(AKNAD1):c.1-24027A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.327 in 149,762 control chromosomes in the GnomAD database, including 9,003 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 0.33 (9003 hom., cov: 24)
• Consequence: AKNAD1 ENST00000357393.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00300

Genes affected

AKNAD1 (HGNC:28398): (AKNA domain containing 1) This gene encodes a protein which contains a domain found in an AT-hook-containing transcription factor. Alternative splicing results in multiple transcript variants. [provided by RefSeq, May 2012]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.506 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
AKNAD1	ENST00000357393.6	c.1-24027A>G		intron_variant		4

Frequencies

GnomAD3 genomes AF: 0.327 AC: 48965 AN: 149652 Hom.: 8992 Cov.: 24

Gnomad AFR AF: 0.151

Gnomad AMI AF: 0.385

Gnomad AMR AF: 0.379

Gnomad ASJ AF: 0.410

Gnomad EAS AF: 0.522

Gnomad SAS AF: 0.501

Gnomad FIN AF: 0.371

Gnomad MID AF: 0.381

Gnomad NFE AF: 0.382

Gnomad OTH AF: 0.385

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

GnomAD4 genome AF: 0.327 AC: 48998 AN: 149762 Hom.: 9003 Cov.: 24 AF XY: 0.332 AC XY: 24234 AN XY: 73008

Gnomad4 AFR AF: 0.151

Gnomad4 AMR AF: 0.379

Gnomad4 ASJ AF: 0.410

Gnomad4 EAS AF: 0.522

Gnomad4 SAS AF: 0.503

Gnomad4 FIN AF: 0.371

Gnomad4 NFE AF: 0.382

Gnomad4 OTH AF: 0.391

Alfa AF: 0.385 Hom.: 15427

Bravo AF: 0.321

Asia WGS AF: 0.514 AC: 1783 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	6.5
Dann	Benign	0.74

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: rs12090453; hg19: chr1-109416225;