chr1-108875057-C-A

Variant names:

• chr1-108875057-C-A
• rs7523050
• ENST00000357393.6:c.1-25481G>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 15 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.279 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.1-25481G>T		intron	N/A	ENSP00000349968.6
	ENSG00000302697	ENST00000788996.1		n.88+83G>T		intron	N/A

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

African (AFR) AF: 0.283 AC: 11663 AN: 41234

American (AMR) AF: 0.141 AC: 2157 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.159 AC: 552 AN: 3468

East Asian (EAS) AF: 0.0491 AC: 254 AN: 5176

South Asian (SAS) AF: 0.156 AC: 750 AN: 4804

European-Finnish (FIN) AF: 0.147 AC: 1540 AN: 10504

Middle Eastern (MID) AF: 0.197 AC: 58 AN: 294

European-Non Finnish (NFE) AF: 0.146 AC: 9910 AN: 67868

Other (OTH) AF: 0.167 AC: 352 AN: 2110

Alfa AF: 0.162 Hom.: 3577

Bravo AF: 0.184

Asia WGS AF: 0.128 AC: 448 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.012
DANN	Benign	0.11
PhyloP100		-0.38
PromoterAI		-0.0079	Neutral
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: rs7523050; hg19: chr1-109417679; COSMIC: COSV51443527; COSMIC: COSV51443527;