rs10773046

Variant names:

• chr12-123890663-A-G
• rs10773046
• NM_001372106.1:c.8996-2570A>G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001372106.1(DNAH10):​c.8996-2570A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.46 in 151,962 control chromosomes in the GnomAD database, including 16,235 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 0.46 (16235 hom., cov: 31)
• Consequence: DNAH10 NM_001372106.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.186

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 Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.499 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DNAH10	NM_001372106.1	c.8996-2570A>G		intron_variant	Intron 52 of 78	ENST00000673944.1	NP_001359035.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DNAH10	ENST00000673944.1	c.8996-2570A>G		intron_variant	Intron 52 of 78		NM_001372106.1	ENSP00000501095.1
DNAH10	ENST00000409039.8	c.8825-2570A>G		intron_variant	Intron 51 of 77	5		ENSP00000386770.4
DNAH10	ENST00000638045.1	c.8642-2570A>G		intron_variant	Intron 51 of 77	5		ENSP00000489675.1

Frequencies

GnomAD3 genomes AF: 0.460 AC: 69798 AN: 151844 Hom.: 16207 Cov.: 31

Gnomad AFR AF: 0.505

Gnomad AMI AF: 0.531

Gnomad AMR AF: 0.441

Gnomad ASJ AF: 0.385

Gnomad EAS AF: 0.281

Gnomad SAS AF: 0.376

Gnomad FIN AF: 0.448

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.462

Gnomad OTH AF: 0.456

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

GnomAD4 genome AF: 0.460 AC: 69880 AN: 151962 Hom.: 16235 Cov.: 31 AF XY: 0.454 AC XY: 33737 AN XY: 74256

Gnomad4 AFR AF: 0.505

Gnomad4 AMR AF: 0.441

Gnomad4 ASJ AF: 0.385

Gnomad4 EAS AF: 0.281

Gnomad4 SAS AF: 0.377

Gnomad4 FIN AF: 0.448

Gnomad4 NFE AF: 0.462

Gnomad4 OTH AF: 0.453

Alfa AF: 0.463 Hom.: 17884

Bravo AF: 0.465

Asia WGS AF: 0.371 AC: 1287 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.3
DANN	Benign	0.24

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

LitVar

Other links and lift over

dbSNP: rs10773046; hg19: chr12-124375210;