rs771542694

Variant names:

• chr1-108834984-G-A
• rs771542694
• NM_152763.5:c.1609C>T

Your query was ambiguous. Multiple possible variants found:

• chr1-108834984-G-A
• chr1-108834984-G-T

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_152763.5(AKNAD1):​c.1609C>T​(p.Gln537*) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000283 in 1,411,386 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Variant results in nonsense mediated mRNA decay.

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.0000028 (0 hom.)
• Consequence: AKNAD1 NM_152763.5 stop_gained
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.84
• Publications: 0 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]

ENSG00000307428 (HGNC:):

ACMG classification

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

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.1609C>T	p.Gln537*	stop_gained	Exon 8 of 16	NP_689976.2	Q5T1N1-1
	AKNAD1	NR_049760.2		n.1958+2566C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AKNAD1	ENST00000370001.8	TSL:1 MANE Select	c.1609C>T	p.Gln537*	stop_gained	Exon 8 of 16	ENSP00000359018.3	Q5T1N1-1
	AKNAD1	ENST00000369995.7	TSL:5	c.1609C>T	p.Gln537*	stop_gained	Exon 8 of 14	ENSP00000359012.3	Q5T1N1-4
	AKNAD1	ENST00000369994.5	TSL:5	c.1537-18C>T		intron	N/A	ENSP00000359011.1	Q5T1N2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD2 exomes AF: 0.0000100 AC: 2 AN: 199952 AF XY: 0.00000907

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.0000931

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.00000283 AC: 4 AN: 1411386 Hom.: 0 Cov.: 31 AF XY: 0.00000285 AC XY: 2 AN XY: 702128

African (AFR) AF: 0.00 AC: 0 AN: 29178

American (AMR) AF: 0.0000640 AC: 2 AN: 31270

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 23948

East Asian (EAS) AF: 0.0000279 AC: 1 AN: 35882

South Asian (SAS) AF: 0.00 AC: 0 AN: 79474

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 53062

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5546

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 1094966

Other (OTH) AF: 0.0000172 AC: 1 AN: 58060

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 0

Bravo AF: 0.0000113

ExAC AF: 0.0000165 AC: 2

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Benign	-0.057	T
BayesDel_noAF	Benign	-0.12
CADD	Uncertain	25
DANN	Benign	0.97
Eigen	Benign	-0.54
Eigen_PC	Benign	-1.0
FATHMM_MKL	Benign	0.0055	N
PhyloP100		-1.8
Vest4		0.024
GERP RS		-4.3
Mutation Taster		=114/86	disease causing (fs/PTC)

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: rs771542694; hg19: chr1-109377606;