chr1-108875057-C-A

Position:

• chr1-108875057-C-A

Variant summary

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

The ENST00000357393.6(AKNAD1):​c.1-25481G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.18 in 151,612 control chromosomes in the GnomAD database, including 2,838 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 0.18 (2838 hom., cov: 31)
• Consequence: AKNAD1 ENST00000357393.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.377

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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.279 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
AKNAD1	ENST00000357393.6	c.1-25481G>T		intron_variant		4		ENSP00000349968

Frequencies

GnomAD3 genomes AF: 0.180 AC: 27311 AN: 151494 Hom.: 2832 Cov.: 31

Gnomad AFR AF: 0.283

Gnomad AMI AF: 0.134

Gnomad AMR AF: 0.141

Gnomad ASJ AF: 0.159

Gnomad EAS AF: 0.0492

Gnomad SAS AF: 0.155

Gnomad FIN AF: 0.147

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.146

Gnomad OTH AF: 0.168

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

GnomAD4 genome AF: 0.180 AC: 27358 AN: 151612 Hom.: 2838 Cov.: 31 AF XY: 0.179 AC XY: 13272 AN XY: 74128

Gnomad4 AFR AF: 0.283

Gnomad4 AMR AF: 0.141

Gnomad4 ASJ AF: 0.159

Gnomad4 EAS AF: 0.0491

Gnomad4 SAS AF: 0.156

Gnomad4 FIN AF: 0.147

Gnomad4 NFE AF: 0.146

Gnomad4 OTH AF: 0.167

Alfa AF: 0.153 Hom.: 2318

Bravo AF: 0.184

Asia WGS AF: 0.128 AC: 448 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.012
DANN	Benign	0.11

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: rs7523050; hg19: chr1-109417679; COSMIC: COSV51443527; COSMIC: COSV51443527;