rs1004330

chr16-70999060-G-A

Variant summary

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

The NM_001270974.2(HYDIN):c.3645-6850C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.313 in 151,860 control chromosomes in the GnomAD database, including 8,790 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 0.31 (8790 hom., cov: 29)
• Consequence: HYDIN NM_001270974.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0740

Genes affected

HYDIN (HGNC:19368): (HYDIN axonemal central pair apparatus protein) This gene encodes a protein that may be involved in cilia motility. Mutations in this gene cause of autosomal recessive primary ciliary dyskinesia-5, a disorder characterized by the accumulation of cerebrospinal fluid within the ventricles of the brain. A duplicate copy of this gene has been found in humans on chromosome 1. [provided by RefSeq, Jan 2013]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.498 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
HYDIN	NM_001270974.2	c.3645-6850C>T		intron_variant		ENST00000393567.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HYDIN	ENST00000393567.7	c.3645-6850C>T		intron_variant		5	NM_001270974.2	P1
HYDIN	ENST00000393552.6	c.2355-6850C>T		intron_variant, NMD_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.313 AC: 47511 AN: 151744 Hom.: 8752 Cov.: 29

Gnomad AFR AF: 0.503

Gnomad AMI AF: 0.131

Gnomad AMR AF: 0.407

Gnomad ASJ AF: 0.244

Gnomad EAS AF: 0.231

Gnomad SAS AF: 0.280

Gnomad FIN AF: 0.201

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.209

Gnomad OTH AF: 0.298

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

GnomAD4 genome AF: 0.313 AC: 47601 AN: 151860 Hom.: 8790 Cov.: 29 AF XY: 0.315 AC XY: 23386 AN XY: 74244

Gnomad4 AFR AF: 0.503

Gnomad4 AMR AF: 0.408

Gnomad4 ASJ AF: 0.244

Gnomad4 EAS AF: 0.231

Gnomad4 SAS AF: 0.278

Gnomad4 FIN AF: 0.201

Gnomad4 NFE AF: 0.209

Gnomad4 OTH AF: 0.298

Alfa AF: 0.261 Hom.: 795

Bravo AF: 0.338

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	1.0
Dann	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1004330; hg19: chr16-71032963;