rs1506069

Variant names:

• chr1-225015494-C-T
• rs1506069
• NM_001367479.1:c.1107+7950C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001367479.1(DNAH14):​c.1107+7950C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.678 in 152,080 control chromosomes in the GnomAD database, including 40,944 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 0.68 (40944 hom., cov: 32)
• Consequence: DNAH14 NM_001367479.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.14
• Publications: 2 publications found

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]

DNAH14 Gene-Disease associations (from GenCC):

• neurodevelopmental disorder

  Inheritance: AR Classification: LIMITED Submitted by: G2P

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.876 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DNAH14	NM_001367479.1	c.1107+7950C>T		intron_variant	Intron 10 of 85	ENST00000682510.1	NP_001354408.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DNAH14	ENST00000682510.1	c.1107+7950C>T		intron_variant	Intron 10 of 85		NM_001367479.1	ENSP00000508305.1

Frequencies

GnomAD3 genomes AF: 0.679 AC: 103136 AN: 151962 Hom.: 40939 Cov.: 32

Gnomad AFR AF: 0.238

Gnomad AMI AF: 0.935

Gnomad AMR AF: 0.735

Gnomad ASJ AF: 0.862

Gnomad EAS AF: 0.695

Gnomad SAS AF: 0.759

Gnomad FIN AF: 0.874

Gnomad MID AF: 0.787

Gnomad NFE AF: 0.882

Gnomad OTH AF: 0.716

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

GnomAD4 genome AF: 0.678 AC: 103148 AN: 152080 Hom.: 40944 Cov.: 32 AF XY: 0.680 AC XY: 50567 AN XY: 74326

African (AFR) AF: 0.238 AC: 9848 AN: 41432

American (AMR) AF: 0.735 AC: 11228 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.862 AC: 2992 AN: 3470

East Asian (EAS) AF: 0.695 AC: 3579 AN: 5150

South Asian (SAS) AF: 0.760 AC: 3667 AN: 4824

European-Finnish (FIN) AF: 0.874 AC: 9260 AN: 10598

Middle Eastern (MID) AF: 0.795 AC: 232 AN: 292

European-Non Finnish (NFE) AF: 0.882 AC: 59980 AN: 68016

Other (OTH) AF: 0.714 AC: 1509 AN: 2114

Alfa AF: 0.763 Hom.: 6021

Bravo AF: 0.648

Asia WGS AF: 0.686 AC: 2384 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.58
DANN	Benign	0.28
PhyloP100		-1.1
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1506069; hg19: chr1-225203196;