rs12024361

chr1-225289789-C-T

Variant summary

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

The NM_001367479.1(DNAH14):c.8272-96C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.343 in 833,904 control chromosomes in the GnomAD database, including 51,337 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 0.31 (8138 hom., cov: 32)
  • Exomes 𝑓: 0.35 (43199 hom.)
• Consequence: DNAH14 NM_001367479.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.666

Genes affected

DNAH14 (HGNC:2945): (dynein axonemal heavy chain 14) Dyneins are microtubule-associated motor protein complexes composed of several heavy, light, and intermediate chains. Two major classes of dyneins, axonemal and cytoplasmic, have been identified. DNAH14 is an axonemal dynein heavy chain (DHC) (Vaughan et al., 1996 [PubMed 8812413]).[supplied by OMIM, Mar 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.43 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DNAH14	NM_001367479.1	c.8272-96C>T		intron_variant		ENST00000682510.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DNAH14	ENST00000682510.1	c.8272-96C>T		intron_variant			NM_001367479.1	P1

Frequencies

GnomAD3 genomes AF: 0.311 AC: 47136 AN: 151758 Hom.: 8132 Cov.: 32

Gnomad AFR AF: 0.156

Gnomad AMI AF: 0.387

Gnomad AMR AF: 0.377

Gnomad ASJ AF: 0.324

Gnomad EAS AF: 0.446

Gnomad SAS AF: 0.441

Gnomad FIN AF: 0.375

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.359

Gnomad OTH AF: 0.311

GnomAD4 exome AF: 0.350 AC: 238790 AN: 682028 Hom.: 43199 AF XY: 0.352 AC XY: 116810 AN XY: 332222

Gnomad4 AFR exome AF: 0.143

Gnomad4 AMR exome AF: 0.386

Gnomad4 ASJ exome AF: 0.335

Gnomad4 EAS exome AF: 0.481

Gnomad4 SAS exome AF: 0.423

Gnomad4 FIN exome AF: 0.390

Gnomad4 NFE exome AF: 0.346

Gnomad4 OTH exome AF: 0.337

GnomAD4 genome AF: 0.310 AC: 47155 AN: 151876 Hom.: 8138 Cov.: 32 AF XY: 0.315 AC XY: 23373 AN XY: 74242

Gnomad4 AFR AF: 0.156

Gnomad4 AMR AF: 0.377

Gnomad4 ASJ AF: 0.324

Gnomad4 EAS AF: 0.445

Gnomad4 SAS AF: 0.440

Gnomad4 FIN AF: 0.375

Gnomad4 NFE AF: 0.359

Gnomad4 OTH AF: 0.314

Alfa AF: 0.323 Hom.: 1344

Bravo AF: 0.303

Asia WGS AF: 0.449 AC: 1561 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	6.1
Dann	Benign	0.65

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: rs12024361; hg19: chr1-225477491;