rs1277203

Variant names:

• chr1-108850215-C-T
• rs1277203
• NM_152763.5:c.994-639G>A

Variant summary

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

The NM_152763.5(AKNAD1):​c.994-639G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.565 in 152,088 control chromosomes in the GnomAD database, including 26,353 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 0.56 (26353 hom., cov: 32)
• Consequence: AKNAD1 NM_152763.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.82
• 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=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.693 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_152763.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AKNAD1	NM_152763.5	MANE Select	c.994-639G>A		intron	N/A	NP_689976.2	Q5T1N1-1
	AKNAD1	NR_049760.2		n.1416-639G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AKNAD1	ENST00000370001.8	TSL:1 MANE Select	c.994-639G>A		intron	N/A	ENSP00000359018.3	Q5T1N1-1
	AKNAD1	ENST00000472781.2	TSL:1	n.994-639G>A		intron	N/A	ENSP00000432262.1	Q5T1N1-2
	AKNAD1	ENST00000369995.7	TSL:5	c.994-639G>A		intron	N/A	ENSP00000359012.3	Q5T1N1-4

Frequencies

GnomAD3 genomes AF: 0.565 AC: 85872 AN: 151970 Hom.: 26340 Cov.: 32

Gnomad AFR AF: 0.303

Gnomad AMI AF: 0.540

Gnomad AMR AF: 0.688

Gnomad ASJ AF: 0.701

Gnomad EAS AF: 0.711

Gnomad SAS AF: 0.703

Gnomad FIN AF: 0.657

Gnomad MID AF: 0.682

Gnomad NFE AF: 0.653

Gnomad OTH AF: 0.627

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

GnomAD4 genome AF: 0.565 AC: 85907 AN: 152088 Hom.: 26353 Cov.: 32 AF XY: 0.572 AC XY: 42571 AN XY: 74360

African (AFR) AF: 0.303 AC: 12547 AN: 41456

American (AMR) AF: 0.689 AC: 10522 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.701 AC: 2431 AN: 3470

East Asian (EAS) AF: 0.712 AC: 3691 AN: 5186

South Asian (SAS) AF: 0.703 AC: 3384 AN: 4816

European-Finnish (FIN) AF: 0.657 AC: 6953 AN: 10586

Middle Eastern (MID) AF: 0.675 AC: 197 AN: 292

European-Non Finnish (NFE) AF: 0.653 AC: 44361 AN: 67978

Other (OTH) AF: 0.629 AC: 1330 AN: 2114

Alfa AF: 0.638 Hom.: 57556

Bravo AF: 0.557

Asia WGS AF: 0.689 AC: 2392 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.013
DANN	Benign	0.59
PhyloP100		-1.8
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: rs1277203; hg19: chr1-109392837;