rs3913653

Variant names:

• chr1-225349369-G-A
• rs3913653
• NM_001367479.1:c.11297-2278G>A

Your query was ambiguous. Multiple possible variants found:

• chr1-225349369-G-A
• chr1-225349369-G-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.11297-2278G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.597 in 151,890 control chromosomes in the GnomAD database, including 28,178 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 0.60 (28178 hom., cov: 31)
• Consequence: DNAH14 NM_001367479.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.28
• Publications: 1 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 (EAS) allele frequency at 95% confidence interval = 0.753 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DNAH14	NM_001367479.1	c.11297-2278G>A		intron_variant	Intron 71 of 85	ENST00000682510.1	NP_001354408.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DNAH14	ENST00000682510.1	c.11297-2278G>A		intron_variant	Intron 71 of 85		NM_001367479.1	ENSP00000508305.1

Frequencies

GnomAD3 genomes AF: 0.597 AC: 90604 AN: 151772 Hom.: 28134 Cov.: 31

Gnomad AFR AF: 0.760

Gnomad AMI AF: 0.566

Gnomad AMR AF: 0.627

Gnomad ASJ AF: 0.388

Gnomad EAS AF: 0.766

Gnomad SAS AF: 0.643

Gnomad FIN AF: 0.495

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.503

Gnomad OTH AF: 0.567

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

GnomAD4 genome AF: 0.597 AC: 90704 AN: 151890 Hom.: 28178 Cov.: 31 AF XY: 0.598 AC XY: 44362 AN XY: 74240

African (AFR) AF: 0.760 AC: 31514 AN: 41450

American (AMR) AF: 0.628 AC: 9581 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.388 AC: 1348 AN: 3470

East Asian (EAS) AF: 0.764 AC: 3950 AN: 5170

South Asian (SAS) AF: 0.642 AC: 3094 AN: 4820

European-Finnish (FIN) AF: 0.495 AC: 5197 AN: 10498

Middle Eastern (MID) AF: 0.435 AC: 127 AN: 292

European-Non Finnish (NFE) AF: 0.503 AC: 34185 AN: 67914

Other (OTH) AF: 0.568 AC: 1193 AN: 2102

Alfa AF: 0.572 Hom.: 4058

Bravo AF: 0.616

Asia WGS AF: 0.708 AC: 2458 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.81
DANN	Benign	0.51
PhyloP100		-1.3
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: rs3913653; hg19: chr1-225537071;