16-70829903-T-C

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_Strong BP6_Moderate

The NM_001270974.2(HYDIN):c.13900-73A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.053 (0 hom., cov: 28)
  • Exomes 𝑓: 0.13 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: HYDIN NM_001270974.2 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.219

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 Likely_benign. Variant got -6 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BP6: Variant 16-70829903-T-C is Benign according to our data. Variant chr16-70829903-T-C is described in ClinVar as [Benign]. Clinvar id is 1685268.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
HYDIN	NM_001270974.2	c.13900-73A>G		intron_variant		ENST00000393567.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HYDIN	ENST00000393567.7	c.13900-73A>G		intron_variant		5	NM_001270974.2	P1
HYDIN	ENST00000378856.8	c.*2656-73A>G		intron_variant, NMD_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.0532 AC: 5361 AN: 100846 Hom.: 0 Cov.: 28

Gnomad AFR AF: 0.0767

Gnomad AMI AF: 0.0704

Gnomad AMR AF: 0.0790

Gnomad ASJ AF: 0.0517

Gnomad EAS AF: 0.0414

Gnomad SAS AF: 0.0330

Gnomad FIN AF: 0.0471

Gnomad MID AF: 0.00391

Gnomad NFE AF: 0.0387

Gnomad OTH AF: 0.0566

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.129 AC: 100333 AN: 774864 Hom.: 0 AF XY: 0.129 AC XY: 50480 AN XY: 391696

Gnomad4 AFR exome AF: 0.177

Gnomad4 AMR exome AF: 0.215

Gnomad4 ASJ exome AF: 0.103

Gnomad4 EAS exome AF: 0.141

Gnomad4 SAS exome AF: 0.0928

Gnomad4 FIN exome AF: 0.165

Gnomad4 NFE exome AF: 0.127

Gnomad4 OTH exome AF: 0.118

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.0531 AC: 5361 AN: 100908 Hom.: 0 Cov.: 28 AF XY: 0.0575 AC XY: 2851 AN XY: 49578

Gnomad4 AFR AF: 0.0765

Gnomad4 AMR AF: 0.0789

Gnomad4 ASJ AF: 0.0517

Gnomad4 EAS AF: 0.0415

Gnomad4 SAS AF: 0.0330

Gnomad4 FIN AF: 0.0471

Gnomad4 NFE AF: 0.0387

Gnomad4 OTH AF: 0.0559

Alfa AF: 0.145 Hom.: 0

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Benign:1

Benign, criteria provided, single submitter

clinical testing

Mendelics

May 04, 2022

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.82
Dann	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1770438; hg19: chr16-70863806; COSMIC: COSV66638517;