rs12047808

Positions:

• chr1-179500179-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_144696.6(AXDND1):​c.2388+7228A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.159 in 151,946 control chromosomes in the GnomAD database, including 2,510 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 0.16 (2510 hom., cov: 31)
• Consequence: AXDND1 NM_144696.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.144

Genes affected

AXDND1 (HGNC:26564): (axonemal dynein light chain domain containing 1)

AXDND1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.275 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
AXDND1	NM_144696.6	c.2388+7228A>G		intron_variant		ENST00000367618.8	NP_653297.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
AXDND1	ENST00000367618.8	c.2388+7228A>G		intron_variant		1	NM_144696.6	ENSP00000356590.3

Frequencies

GnomAD3 genomes AF: 0.159 AC: 24105 AN: 151828 Hom.: 2506 Cov.: 31

Gnomad AFR AF: 0.279

Gnomad AMI AF: 0.129

Gnomad AMR AF: 0.106

Gnomad ASJ AF: 0.0953

Gnomad EAS AF: 0.155

Gnomad SAS AF: 0.0298

Gnomad FIN AF: 0.142

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.114

Gnomad OTH AF: 0.148

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

GnomAD4 genome AF: 0.159 AC: 24135 AN: 151946 Hom.: 2510 Cov.: 31 AF XY: 0.156 AC XY: 11620 AN XY: 74262

Gnomad4 AFR AF: 0.279

Gnomad4 AMR AF: 0.106

Gnomad4 ASJ AF: 0.0953

Gnomad4 EAS AF: 0.155

Gnomad4 SAS AF: 0.0290

Gnomad4 FIN AF: 0.142

Gnomad4 NFE AF: 0.114

Gnomad4 OTH AF: 0.151

Alfa AF: 0.118 Hom.: 2608

Bravo AF: 0.164

Asia WGS AF: 0.0920 AC: 321 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	3.0
DANN	Benign	0.21

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: rs12047808; hg19: chr1-179469314;