rs1007173839

Variant names:

• chr2-68134771-C-G
• NM_138458.4:c.797G>C

Your query was ambiguous. Multiple possible variants found:

• chr2-68134771-C-G
• chr2-68134771-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_138458.4(DNAAF10):​c.797G>C​(p.Arg266Pro) variant causes a missense change. The variant allele was found at a frequency of 0.000000685 in 1,459,034 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R266Q) has been classified as Uncertain significance.

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 6.9e-7 (0 hom.)
• Consequence: DNAAF10 NM_138458.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 5.05

Genes affected

DNAAF10 (HGNC:25176): (dynein axonemal assembly factor 10) This gene encodes a protein with two WD40 repeat domains thought to be involved in an apoptosis via activation of caspase-3. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Feb 2012]

ENSG00000273398 (HGNC:):

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DNAAF10	NM_138458.4	c.797G>C	p.Arg266Pro	missense_variant	Exon 7 of 8	ENST00000295121.11	NP_612467.1
DNAAF10	NM_001256476.2	c.797G>C	p.Arg266Pro	missense_variant	Exon 7 of 7		NP_001243405.1
DNAAF10	NR_046234.2	n.768G>C		non_coding_transcript_exon_variant	Exon 7 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DNAAF10	ENST00000295121.11	c.797G>C	p.Arg266Pro	missense_variant	Exon 7 of 8	1	NM_138458.4	ENSP00000295121.6
ENSG00000273398	ENST00000406334.3	n.*814G>C		non_coding_transcript_exon_variant	Exon 14 of 15	2		ENSP00000384974.3
ENSG00000273398	ENST00000406334.3	n.*814G>C		3_prime_UTR_variant	Exon 14 of 15	2		ENSP00000384974.3

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 6.85e-7 AC: 1 AN: 1459034 Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0 AN XY: 725852

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 9.00e-7

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.97
BayesDel_addAF	Pathogenic	0.42	D
BayesDel_noAF	Pathogenic	0.37
CADD	Pathogenic	28
DANN	Uncertain	0.99
DEOGEN2	Benign	0.061	T;.;.
Eigen	Uncertain	0.67
Eigen_PC	Pathogenic	0.68
FATHMM_MKL	Uncertain	0.96	D
LIST_S2	Uncertain	0.87	D;D;D
M_CAP	Uncertain	0.12	D
MetaRNN	Uncertain	0.66	D;D;D
MetaSVM	Uncertain	0.59	D
MutationAssessor	Uncertain	2.7	M;.;M
PrimateAI	Uncertain	0.59	T
PROVEAN	Pathogenic	-5.0	D;D;D
REVEL	Uncertain	0.61
Sift	Uncertain	0.0060	D;T;D
Sift4G	Benign	0.19	T;T;T
Polyphen		1.0	D;.;.
Vest4		0.79
MutPred		0.62		Loss of MoRF binding (P = 0.0012);.;Loss of MoRF binding (P = 0.0012);
MVP		0.79
MPC		1.1
ClinPred		0.99	D
GERP RS		5.7
Varity_R		0.90
gMVP		0.88

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr2-68361903;