5-13957203-G-A

Position:

• chr5-13957203-G-A

Variant summary

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

The ENST00000681290.1(DNAH5):​c.13-25959C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0424 in 152,180 control chromosomes in the GnomAD database, including 155 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 0.042 (155 hom., cov: 33)
• Consequence: DNAH5 ENST00000681290.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.162

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0636 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DNAH5	XM_005248262.4	c.166-25959C>T		intron_variant
DNAH5	XM_017009177.2	c.166-25959C>T		intron_variant
DNAH5	XM_017009180.2	c.166-25959C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DNAH5	ENST00000681290.1	c.13-25959C>T		intron_variant				A1

Frequencies

GnomAD3 genomes AF: 0.0424 AC: 6450 AN: 152062 Hom.: 155 Cov.: 33

Gnomad AFR AF: 0.0658

Gnomad AMI AF: 0.0362

Gnomad AMR AF: 0.0447

Gnomad ASJ AF: 0.0325

Gnomad EAS AF: 0.0397

Gnomad SAS AF: 0.0460

Gnomad FIN AF: 0.0445

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0281

Gnomad OTH AF: 0.0383

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

GnomAD4 genome AF: 0.0424 AC: 6453 AN: 152180 Hom.: 155 Cov.: 33 AF XY: 0.0427 AC XY: 3179 AN XY: 74398

Gnomad4 AFR AF: 0.0657

Gnomad4 AMR AF: 0.0445

Gnomad4 ASJ AF: 0.0325

Gnomad4 EAS AF: 0.0396

Gnomad4 SAS AF: 0.0465

Gnomad4 FIN AF: 0.0445

Gnomad4 NFE AF: 0.0281

Gnomad4 OTH AF: 0.0379

Alfa AF: 0.0389 Hom.: 47

Bravo AF: 0.0419

Asia WGS AF: 0.0500 AC: 174 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.39
DANN	Benign	0.55

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs16902967; hg19: chr5-13957312;