1-179500179-A-G

Variant names:

• chr1-179500179-A-G
• rs12047808
• NM_144696.6:c.2388+7228A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 11 publications found

Genes affected

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

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 (AFR) allele frequency at 95% confidence interval = 0.275 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_144696.6. 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
	AXDND1	NM_144696.6	MANE Select	c.2388+7228A>G		intron	N/A	NP_653297.3
	AXDND1	NR_073544.2		n.2343-6654A>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AXDND1	ENST00000367618.8	TSL:1 MANE Select	c.2388+7228A>G		intron	N/A	ENSP00000356590.3
	AXDND1	ENST00000434088.1	TSL:1	c.2190+7228A>G		intron	N/A	ENSP00000391716.1
	AXDND1	ENST00000511157.5	TSL:1	n.*564-6654A>G		intron	N/A	ENSP00000424373.1

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

African (AFR) AF: 0.279 AC: 11558 AN: 41420

American (AMR) AF: 0.106 AC: 1622 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.0953 AC: 331 AN: 3472

East Asian (EAS) AF: 0.155 AC: 803 AN: 5170

South Asian (SAS) AF: 0.0290 AC: 140 AN: 4826

European-Finnish (FIN) AF: 0.142 AC: 1500 AN: 10562

Middle Eastern (MID) AF: 0.0986 AC: 29 AN: 294

European-Non Finnish (NFE) AF: 0.114 AC: 7718 AN: 67930

Other (OTH) AF: 0.151 AC: 316 AN: 2098

Alfa AF: 0.126 Hom.: 6308

Bravo AF: 0.164

Asia WGS AF: 0.0920 AC: 321 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	0.21
PhyloP100		0.14
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: rs12047808; hg19: chr1-179469314;