Variant chr6-158993779-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_031924.8(RSPH3):c.204+60G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.11 in 889,040 control chromosomes in the GnomAD database, including 10,777 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.11 ( 1725 hom., cov: 32)

Exomes 𝑓: 0.11 ( 9052 hom. )

Consequence

RSPH3
NM_031924.8 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.546

Variant links:

Genes affected

RSPH3 (HGNC:21054): (radial spoke head 3) The protein encoded by this gene acts as a protein kinase A anchoring protein. Mutations in this gene cause primary ciliary dyskinesia; a disorder characterized by defects of the axoneme in motile cilia and sperm flagella. The homolog of this gene was first identified in the blue-green algae Chlamydomonas as encoding a radial spoke protein that formed a structural component of motile cilia and flagella. Alternate splicing results in multiple transcript variants encoding distinct isoforms. [provided by RefSeq, Dec 2016]

RSPH3 links:

TAGAP-AS1 (HGNC:55239): (TAGAP antisense RNA 1)

TAGAP-AS1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.83).

BP6

Variant 6-158993779-C-T is Benign according to our data. Variant chr6-158993779-C-T is described in ClinVar as [Benign]. Clinvar id is 1236074.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.401 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RSPH3	NM_031924.8 linkuse as main transcript	c.204+60G>A		intron_variant		ENST00000367069.7	NP_114130.4

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	Appris
RSPH3	ENST00000367069.7 linkuse as main transcript	c.204+60G>A	intron_variant	1	NM_031924.8	ENSP00000356036	P1
RSPH3	ENST00000449822.5 linkuse as main transcript	c.204+60G>A	intron_variant	2		ENSP00000393195
TAGAP-AS1	ENST00000607391.5 linkuse as main transcript	n.236+3207C>T	intron_variant, non_coding_transcript_variant	3

Frequencies

GnomAD3 genomes

AF:

0.114

AC:

17346

AN:

152060

Hom.:

1714

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0751

Gnomad AMI

AF:

0.0515

Gnomad AMR

AF:

0.282

Gnomad ASJ

AF:

0.108

Gnomad EAS

AF:

0.415

Gnomad SAS

AF:

0.194

Gnomad FIN

AF:

0.0914

Gnomad MID

AF:

0.101

Gnomad NFE

AF:

0.0758

Gnomad OTH

AF:

0.125

GnomAD4 exome

AF:

0.109

AC:

80567

AN:

736862

Hom.:

9052

AF XY:

0.109

AC XY:

42065

AN XY:

387554

show subpopulations

Gnomad4 AFR exome

AF:

0.0608

Gnomad4 AMR exome

AF:

0.415

Gnomad4 ASJ exome

AF:

0.0973

Gnomad4 EAS exome

AF:

0.462

Gnomad4 SAS exome

AF:

0.149

Gnomad4 FIN exome

AF:

0.0855

Gnomad4 NFE exome

AF:

0.0668

Gnomad4 OTH exome

AF:

0.108

GnomAD4 genome

AF:

0.114

AC:

17392

AN:

152178

Hom.:

1725

Cov.:

AF XY:

0.120

AC XY:

8937

AN XY:

74404

show subpopulations

Gnomad4 AFR

AF:

0.0756

Gnomad4 AMR

AF:

0.282

Gnomad4 ASJ

AF:

0.108

Gnomad4 EAS

AF:

0.416

Gnomad4 SAS

AF:

0.194

Gnomad4 FIN

AF:

0.0914

Gnomad4 NFE

AF:

0.0758

Gnomad4 OTH

AF:

0.130

Alfa

AF:

0.0318

Hom.:

Bravo

AF:

0.133

Asia WGS

AF:

0.281

AC:

978

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Nov 12, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

0.72

DANN

Benign

0.71

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over