5-13986994-A-G

Variant names:

• chr5-13986994-A-G
• rs1031006
• ENST00000827039.1:n.338A>G

Variant summary

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

The ENST00000827039.1(ENSG00000307550):​n.338A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.39 in 151,960 control chromosomes in the GnomAD database, including 11,877 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 0.39 (11877 hom., cov: 31)
• Consequence: ENSG00000307550 ENST00000827039.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.78
• Publications: 5 publications found

Genes affected

ENSG00000307550 (HGNC:):

DNAH5 (HGNC:2950): (dynein axonemal heavy chain 5) This gene encodes a dynein protein, which is part of a microtubule-associated motor protein complex consisting of heavy, light, and intermediate chains. This protein is an axonemal heavy chain dynein. It functions as a force-generating protein with ATPase activity, whereby the release of ADP is thought to produce the force-producing power stroke. Mutations in this gene cause primary ciliary dyskinesia type 3, as well as Kartagener syndrome, which are both diseases due to ciliary defects. [provided by RefSeq, Oct 2009]

DNAH5 Gene-Disease associations (from GenCC):

• primary ciliary dyskinesia 3

  Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: PanelApp Australia, Labcorp Genetics (formerly Invitae), G2P, ClinGen
• primary ciliary dyskinesia

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.07).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.662 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DNAH5	XM_005248262.4	c.165+24654T>C		intron_variant	Intron 1 of 78		XP_005248319.2
DNAH5	XM_017009177.2	c.165+24654T>C		intron_variant	Intron 1 of 76		XP_016864666.1
DNAH5	XM_017009180.2	c.165+24654T>C		intron_variant	Intron 1 of 73		XP_016864669.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000307550	ENST00000827039.1	n.338A>G		non_coding_transcript_exon_variant	Exon 2 of 2
DNAH5	ENST00000681290.1	c.12+24654T>C		intron_variant	Intron 1 of 78			ENSP00000505288.1

Frequencies

GnomAD3 genomes AF: 0.390 AC: 59200 AN: 151842 Hom.: 11862 Cov.: 31

Gnomad AFR AF: 0.437

Gnomad AMI AF: 0.364

Gnomad AMR AF: 0.382

Gnomad ASJ AF: 0.337

Gnomad EAS AF: 0.681

Gnomad SAS AF: 0.324

Gnomad FIN AF: 0.346

Gnomad MID AF: 0.402

Gnomad NFE AF: 0.356

Gnomad OTH AF: 0.377

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

GnomAD4 genome AF: 0.390 AC: 59262 AN: 151960 Hom.: 11877 Cov.: 31 AF XY: 0.390 AC XY: 28963 AN XY: 74274

African (AFR) AF: 0.437 AC: 18111 AN: 41418

American (AMR) AF: 0.382 AC: 5839 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.337 AC: 1168 AN: 3470

East Asian (EAS) AF: 0.681 AC: 3505 AN: 5146

South Asian (SAS) AF: 0.322 AC: 1553 AN: 4816

European-Finnish (FIN) AF: 0.346 AC: 3655 AN: 10550

Middle Eastern (MID) AF: 0.405 AC: 119 AN: 294

European-Non Finnish (NFE) AF: 0.356 AC: 24184 AN: 67976

Other (OTH) AF: 0.379 AC: 797 AN: 2104

Alfa AF: 0.357 Hom.: 17109

Bravo AF: 0.395

Asia WGS AF: 0.509 AC: 1770 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.19
DANN	Benign	0.22
PhyloP100		-1.8

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1031006; hg19: chr5-13987103;