chr1-108873603-T-C

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

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]

ENSG00000302697 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000357393.6. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AKNAD1	ENST00000357393.6	TSL:4	c.1-24027A>G		intron	N/A	ENSP00000349968.6
	ENSG00000302697	ENST00000788996.1		n.88+1537A>G		intron	N/A

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

African (AFR) AF: 0.151 AC: 6160 AN: 40844

American (AMR) AF: 0.379 AC: 5668 AN: 14954

Ashkenazi Jewish (ASJ) AF: 0.410 AC: 1414 AN: 3448

East Asian (EAS) AF: 0.522 AC: 2617 AN: 5010

South Asian (SAS) AF: 0.503 AC: 2360 AN: 4694

European-Finnish (FIN) AF: 0.371 AC: 3772 AN: 10162

Middle Eastern (MID) AF: 0.378 AC: 109 AN: 288

European-Non Finnish (NFE) AF: 0.382 AC: 25751 AN: 67416

Other (OTH) AF: 0.391 AC: 801 AN: 2048

Alfa AF: 0.382 Hom.: 19399

Bravo AF: 0.321

Asia WGS AF: 0.514 AC: 1783 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	6.5
DANN	Benign	0.74
PhyloP100		-0.0030
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs12090453; hg19: chr1-109416225;