rs12090453

Variant names:

• chr1-108873603-T-C
• rs12090453
• ENST00000357393.6:c.1-24027A>G

Your query was ambiguous. Multiple possible variants found:

• chr1-108873603-T-C
• chr1-108873603-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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
AKNAD1	ENST00000357393.6	c.1-24027A>G		intron_variant	Intron 1 of 5	4		ENSP00000349968.6

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;