1-108856295-G-T

Variant names:

• chr1-108856295-G-T
• rs17621621
• NM_152763.5:c.-104+634C>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000370001.8(AKNAD1):​c.-104+634C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.123 in 152,018 control chromosomes in the GnomAD database, including 1,268 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 0.12 (1268 hom., cov: 31)
• Consequence: AKNAD1 ENST00000370001.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0280
• 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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.14 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000370001.8. 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
	AKNAD1	NM_152763.5	MANE Select	c.-104+634C>A		intron	N/A	NP_689976.2
	AKNAD1	NR_049760.2		n.319+634C>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AKNAD1	ENST00000370001.8	TSL:1 MANE Select	c.-104+634C>A		intron	N/A	ENSP00000359018.3
	AKNAD1	ENST00000472781.2	TSL:1	n.-104+634C>A		intron	N/A	ENSP00000432262.1
	AKNAD1	ENST00000369995.7	TSL:5	c.-104+634C>A		intron	N/A	ENSP00000359012.3

Frequencies

GnomAD3 genomes AF: 0.123 AC: 18756 AN: 151900 Hom.: 1267 Cov.: 31

Gnomad AFR AF: 0.0946

Gnomad AMI AF: 0.135

Gnomad AMR AF: 0.118

Gnomad ASJ AF: 0.167

Gnomad EAS AF: 0.0304

Gnomad SAS AF: 0.134

Gnomad FIN AF: 0.145

Gnomad MID AF: 0.162

Gnomad NFE AF: 0.143

Gnomad OTH AF: 0.124

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

GnomAD4 genome AF: 0.123 AC: 18772 AN: 152018 Hom.: 1268 Cov.: 31 AF XY: 0.123 AC XY: 9160 AN XY: 74276

African (AFR) AF: 0.0946 AC: 3922 AN: 41454

American (AMR) AF: 0.118 AC: 1797 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.167 AC: 580 AN: 3470

East Asian (EAS) AF: 0.0303 AC: 157 AN: 5182

South Asian (SAS) AF: 0.135 AC: 648 AN: 4816

European-Finnish (FIN) AF: 0.145 AC: 1528 AN: 10526

Middle Eastern (MID) AF: 0.158 AC: 46 AN: 292

European-Non Finnish (NFE) AF: 0.143 AC: 9712 AN: 68000

Other (OTH) AF: 0.123 AC: 259 AN: 2106

Alfa AF: 0.134 Hom.: 1307

Bravo AF: 0.119

Asia WGS AF: 0.0920 AC: 323 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	3.0
DANN	Benign	0.40
PhyloP100		-0.028
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: rs17621621; hg19: chr1-109398917;