rs191384577

Variant names:

• chr12-123909293-C-A
• NM_001372106.1:c.9848C>A

Your query was ambiguous. Multiple possible variants found:

• chr12-123909293-C-A
• chr12-123909293-C-G
• chr12-123909293-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2 BP4

The NM_001372106.1(DNAH10):​c.9848C>A​(p.Thr3283Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 12/19 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 32)
• Consequence: DNAH10 NM_001372106.1 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.13

Genes affected

DNAH10 (HGNC:2941): (dynein axonemal heavy chain 10) Dyneins are microtubule-associated motor protein complexes composed of several heavy, light, and intermediate chains. The axonemal dyneins, found in cilia and flagella, are components of the outer and inner dynein arms attached to the peripheral microtubule doublets. DNAH10 is an inner arm dynein heavy chain (Maiti et al., 2000 [PubMed 11175280]).[supplied by OMIM, Mar 2008]

ACMG classification

Verdict is Uncertain_significance. Variant got 1 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.3088562).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DNAH10	NM_001372106.1	c.9848C>A	p.Thr3283Lys	missense_variant	Exon 58 of 79	ENST00000673944.1	NP_001359035.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DNAH10	ENST00000673944.1	c.9848C>A	p.Thr3283Lys	missense_variant	Exon 58 of 79		NM_001372106.1	ENSP00000501095.1
DNAH10	ENST00000409039.8	c.9677C>A	p.Thr3226Lys	missense_variant	Exon 57 of 78	5		ENSP00000386770.4
DNAH10	ENST00000638045.1	c.9494C>A	p.Thr3165Lys	missense_variant	Exon 57 of 78	5		ENSP00000489675.1
DNAH10	ENST00000540041.2	c.233C>A	p.Thr78Lys	missense_variant	Exon 2 of 5	5		ENSP00000445308.2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Uncertain	0.37
BayesDel_addAF	Benign	-0.014	T
BayesDel_noAF	Benign	-0.26
CADD	Benign	20
DANN	Benign	0.87
DEOGEN2	Benign	0.23	.;T;.
Eigen	Benign	-0.17
Eigen_PC	Benign	0.052
FATHMM_MKL	Uncertain	0.94	D
LIST_S2	Uncertain	0.90	D;D;.
M_CAP	Benign	0.016	T
MetaRNN	Benign	0.31	T;T;T
MetaSVM	Benign	-0.90	T
MutationAssessor	Benign	1.7	.;L;.
PrimateAI	Uncertain	0.58	T
REVEL	Benign	0.26
Sift4G	Uncertain	0.0070	.;.;D
Polyphen		0.039	.;B;.
MutPred		0.50		.;Gain of methylation at T3165 (P = 0.0124);.;
MVP		0.50
MPC		0.18
ClinPred		0.71	D
GERP RS		5.6
Varity_R		0.23
gMVP		0.68

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: chr12-124393840;