rs1506069

Positions:

• chr1-225015494-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.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

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=-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/exons	MANE	UniProt
DNAH14	NM_001367479.1	c.1107+7950C>T		intron_variant		ENST00000682510.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DNAH14	ENST00000682510.1	c.1107+7950C>T		intron_variant			NM_001367479.1	P1

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

Gnomad4 AFR AF: 0.238

Gnomad4 AMR AF: 0.735

Gnomad4 ASJ AF: 0.862

Gnomad4 EAS AF: 0.695

Gnomad4 SAS AF: 0.760

Gnomad4 FIN AF: 0.874

Gnomad4 NFE AF: 0.882

Gnomad4 OTH AF: 0.714

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

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: rs1506069; hg19: chr1-225203196;