rs1277203

Positions:

• chr1-108850215-C-T

Variant summary

Our verdict is Benign. Variant got -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

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=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.693 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
AKNAD1	NM_152763.5	c.994-639G>A		intron_variant		ENST00000370001.8	NP_689976.2
AKNAD1	NR_049760.2	n.1416-639G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
AKNAD1	ENST00000370001.8	c.994-639G>A		intron_variant		1	NM_152763.5	ENSP00000359018	P2

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

Gnomad4 AFR AF: 0.303

Gnomad4 AMR AF: 0.689

Gnomad4 ASJ AF: 0.701

Gnomad4 EAS AF: 0.712

Gnomad4 SAS AF: 0.703

Gnomad4 FIN AF: 0.657

Gnomad4 NFE AF: 0.653

Gnomad4 OTH AF: 0.629

Alfa AF: 0.649 Hom.: 42559

Bravo AF: 0.557

Asia WGS AF: 0.689 AC: 2392 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.013
DANN	Benign	0.59

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: rs1277203; hg19: chr1-109392837;