rs6666455

Variant names:

• chr1-179370280-G-A
• rs6666455
• NM_144696.6:c.374+202G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_144696.6(AXDND1):​c.374+202G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.325 in 152,076 control chromosomes in the GnomAD database, including 8,468 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 0.33 (8468 hom., cov: 33)
• Consequence: AXDND1 NM_144696.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.215
• Publications: 4 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=-0.78).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.375 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AXDND1	NM_144696.6	MANE Select	c.374+202G>A		intron	N/A	NP_653297.3
	AXDND1	NR_073544.2		n.563+202G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AXDND1	ENST00000367618.8	TSL:1 MANE Select	c.374+202G>A		intron	N/A	ENSP00000356590.3	Q5T1B0-1
	AXDND1	ENST00000434088.1	TSL:1	c.176+202G>A		intron	N/A	ENSP00000391716.1	B1AM31
	AXDND1	ENST00000511157.5	TSL:1	n.374+202G>A		intron	N/A	ENSP00000424373.1	A6H900

Frequencies

GnomAD3 genomes AF: 0.325 AC: 49405 AN: 151956 Hom.: 8463 Cov.: 33

Gnomad AFR AF: 0.214

Gnomad AMI AF: 0.382

Gnomad AMR AF: 0.371

Gnomad ASJ AF: 0.320

Gnomad EAS AF: 0.358

Gnomad SAS AF: 0.373

Gnomad FIN AF: 0.295

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.379

Gnomad OTH AF: 0.348

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

GnomAD4 genome AF: 0.325 AC: 49431 AN: 152076 Hom.: 8468 Cov.: 33 AF XY: 0.323 AC XY: 24010 AN XY: 74358

African (AFR) AF: 0.214 AC: 8876 AN: 41488

American (AMR) AF: 0.371 AC: 5657 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.320 AC: 1111 AN: 3470

East Asian (EAS) AF: 0.359 AC: 1857 AN: 5176

South Asian (SAS) AF: 0.374 AC: 1805 AN: 4824

European-Finnish (FIN) AF: 0.295 AC: 3125 AN: 10586

Middle Eastern (MID) AF: 0.442 AC: 129 AN: 292

European-Non Finnish (NFE) AF: 0.379 AC: 25779 AN: 67958

Other (OTH) AF: 0.352 AC: 745 AN: 2116

Alfa AF: 0.341 Hom.: 1531

Bravo AF: 0.327

Asia WGS AF: 0.389 AC: 1354 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	2.3
DANN	Benign	0.67
PhyloP100		-0.21
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: rs6666455; hg19: chr1-179339415;