chr6-158993576-C-T

Position:

• chr6-158993576-C-T

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_031924.8(RSPH3):​c.204+263G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.111 in 151,856 control chromosomes in the GnomAD database, including 2,281 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.11 (2281 hom., cov: 31)
• Consequence: RSPH3 NM_031924.8 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.68

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]

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

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BP6: Variant 6-158993576-C-T is Benign according to our data. Variant chr6-158993576-C-T is described in ClinVar as [Benign]. Clinvar id is 1277426.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.325 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RSPH3	NM_031924.8	c.204+263G>A		intron_variant		ENST00000367069.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RSPH3	ENST00000367069.7	c.204+263G>A		intron_variant		1	NM_031924.8	P1
RSPH3	ENST00000449822.5	c.204+263G>A		intron_variant		2
TAGAP-AS1	ENST00000607391.5	n.236+3004C>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.111 AC: 16892 AN: 151738 Hom.: 2272 Cov.: 31

Gnomad AFR AF: 0.330

Gnomad AMI AF: 0.00548

Gnomad AMR AF: 0.0467

Gnomad ASJ AF: 0.0156

Gnomad EAS AF: 0.000770

Gnomad SAS AF: 0.0335

Gnomad FIN AF: 0.0339

Gnomad MID AF: 0.0573

Gnomad NFE AF: 0.0263

Gnomad OTH AF: 0.0987

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

GnomAD4 genome AF: 0.111 AC: 16929 AN: 151856 Hom.: 2281 Cov.: 31 AF XY: 0.109 AC XY: 8063 AN XY: 74218

Gnomad4 AFR AF: 0.330

Gnomad4 AMR AF: 0.0466

Gnomad4 ASJ AF: 0.0156

Gnomad4 EAS AF: 0.000772

Gnomad4 SAS AF: 0.0329

Gnomad4 FIN AF: 0.0339

Gnomad4 NFE AF: 0.0263

Gnomad4 OTH AF: 0.0972

Alfa AF: 0.0551 Hom.: 186

Bravo AF: 0.123

Asia WGS AF: 0.0390 AC: 135 AN: 3476

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Mar 25, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.0080
DANN	Benign	0.54

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

Other links and lift over

dbSNP: rs79073226; hg19: chr6-159414608;