chr1-179548231-A-G

Variant names:

• chr1-179548231-A-G
• rs928016
• NM_144696.6:c.3032-6281A>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.3032-6281A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.907 in 152,216 control chromosomes in the GnomAD database, including 62,804 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 0.91 (62804 hom., cov: 32)
• Consequence: AXDND1 NM_144696.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.557
• Publications: 2 publications found

Genes affected

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

ENSG00000261250 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.942 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
AXDND1	NM_144696.6	c.3032-6281A>G		intron_variant	Intron 25 of 25	ENST00000367618.8	NP_653297.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
AXDND1	ENST00000367618.8	c.3032-6281A>G		intron_variant	Intron 25 of 25	1	NM_144696.6	ENSP00000356590.3

Frequencies

GnomAD3 genomes AF: 0.907 AC: 138003 AN: 152098 Hom.: 62763 Cov.: 32

Gnomad AFR AF: 0.852

Gnomad AMI AF: 0.876

Gnomad AMR AF: 0.936

Gnomad ASJ AF: 0.904

Gnomad EAS AF: 0.963

Gnomad SAS AF: 0.878

Gnomad FIN AF: 0.931

Gnomad MID AF: 0.880

Gnomad NFE AF: 0.930

Gnomad OTH AF: 0.893

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

GnomAD4 genome AF: 0.907 AC: 138102 AN: 152216 Hom.: 62804 Cov.: 32 AF XY: 0.907 AC XY: 67534 AN XY: 74420

African (AFR) AF: 0.852 AC: 35355 AN: 41502

American (AMR) AF: 0.936 AC: 14319 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.904 AC: 3137 AN: 3470

East Asian (EAS) AF: 0.964 AC: 4993 AN: 5180

South Asian (SAS) AF: 0.878 AC: 4231 AN: 4818

European-Finnish (FIN) AF: 0.931 AC: 9886 AN: 10618

Middle Eastern (MID) AF: 0.881 AC: 259 AN: 294

European-Non Finnish (NFE) AF: 0.930 AC: 63234 AN: 68018

Other (OTH) AF: 0.895 AC: 1891 AN: 2114

Alfa AF: 0.915 Hom.: 17243

Bravo AF: 0.907

Asia WGS AF: 0.915 AC: 3182 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	3.6
DANN	Benign	0.81
PhyloP100		-0.56
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: rs928016; hg19: chr1-179517366;