rs10513153

Variant names:

• chr5-13769891-C-T
• rs10513153
• NM_001369.3:c.9606-276G>A

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_001369.3(DNAH5):​c.9606-276G>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 152,028 control chromosomes in the GnomAD database, including 8,255 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.32 (8255 hom., cov: 34)
• Consequence: DNAH5 NM_001369.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.977

Genes affected

DNAH5 (HGNC:2950): (dynein axonemal heavy chain 5) This gene encodes a dynein protein, which is part of a microtubule-associated motor protein complex consisting of heavy, light, and intermediate chains. This protein is an axonemal heavy chain dynein. It functions as a force-generating protein with ATPase activity, whereby the release of ADP is thought to produce the force-producing power stroke. Mutations in this gene cause primary ciliary dyskinesia type 3, as well as Kartagener syndrome, which are both diseases due to ciliary defects. [provided by RefSeq, Oct 2009]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BP6: Variant 5-13769891-C-T is Benign according to our data. Variant chr5-13769891-C-T is described in ClinVar as [Benign]. Clinvar id is 1235747.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.362 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DNAH5	NM_001369.3	c.9606-276G>A		intron_variant	Intron 56 of 78	ENST00000265104.5	NP_001360.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DNAH5	ENST00000265104.5	c.9606-276G>A		intron_variant	Intron 56 of 78	1	NM_001369.3	ENSP00000265104.4
DNAH5	ENST00000681290.1	c.9561-276G>A		intron_variant	Intron 56 of 78			ENSP00000505288.1
DNAH5	ENST00000504001.3	n.318-276G>A		intron_variant	Intron 2 of 4	5

Frequencies

GnomAD3 genomes AF: 0.325 AC: 49372 AN: 151910 Hom.: 8256 Cov.: 34

Gnomad AFR AF: 0.251

Gnomad AMI AF: 0.461

Gnomad AMR AF: 0.346

Gnomad ASJ AF: 0.362

Gnomad EAS AF: 0.327

Gnomad SAS AF: 0.241

Gnomad FIN AF: 0.327

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.366

Gnomad OTH AF: 0.347

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

GnomAD4 genome AF: 0.325 AC: 49378 AN: 152028 Hom.: 8255 Cov.: 34 AF XY: 0.324 AC XY: 24045 AN XY: 74286

Gnomad4 AFR AF: 0.251

Gnomad4 AMR AF: 0.346

Gnomad4 ASJ AF: 0.362

Gnomad4 EAS AF: 0.327

Gnomad4 SAS AF: 0.238

Gnomad4 FIN AF: 0.327

Gnomad4 NFE AF: 0.366

Gnomad4 OTH AF: 0.345

Alfa AF: 0.362 Hom.: 12866

Bravo AF: 0.326

Asia WGS AF: 0.284 AC: 987 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Nov 10, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.66
DANN	Benign	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

LitVar

Other links and lift over

dbSNP: rs10513153; hg19: chr5-13770000;