rs10495234

Positions:

• chr1-225305881-G-A
• chr1-225305881-G-T

Variant summary

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

The NM_001367479.1(DNAH14):​c.9005+792G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.291 in 152,142 control chromosomes in the GnomAD database, including 7,119 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 0.29 (7119 hom., cov: 33)
• Consequence: DNAH14 NM_001367479.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.103

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=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.42 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DNAH14	NM_001367479.1	c.9005+792G>A		intron_variant		ENST00000682510.1	NP_001354408.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DNAH14	ENST00000682510.1	c.9005+792G>A		intron_variant			NM_001367479.1	ENSP00000508305	P1

Frequencies

GnomAD3 genomes AF: 0.291 AC: 44224 AN: 152022 Hom.: 7111 Cov.: 33

Gnomad AFR AF: 0.151

Gnomad AMI AF: 0.364

Gnomad AMR AF: 0.359

Gnomad ASJ AF: 0.245

Gnomad EAS AF: 0.436

Gnomad SAS AF: 0.421

Gnomad FIN AF: 0.358

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.331

Gnomad OTH AF: 0.292

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

GnomAD4 genome AF: 0.291 AC: 44247 AN: 152142 Hom.: 7119 Cov.: 33 AF XY: 0.296 AC XY: 21996 AN XY: 74384

Gnomad4 AFR AF: 0.151

Gnomad4 AMR AF: 0.359

Gnomad4 ASJ AF: 0.245

Gnomad4 EAS AF: 0.435

Gnomad4 SAS AF: 0.420

Gnomad4 FIN AF: 0.358

Gnomad4 NFE AF: 0.331

Gnomad4 OTH AF: 0.295

Alfa AF: 0.322 Hom.: 4409

Bravo AF: 0.283

Asia WGS AF: 0.426 AC: 1482 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.4
DANN	Benign	0.50

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.040		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: rs10495234; hg19: chr1-225493583;