21-42475587-T-C

Position:

• chr21-42475587-T-C

Variant summary

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

The NM_080860.4(RSPH1):​c.877+311A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.219 in 141,378 control chromosomes in the GnomAD database, including 3,976 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.22 (3976 hom., cov: 22)
• Consequence: RSPH1 NM_080860.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -3.46

Genes affected

RSPH1 (HGNC:12371): (radial spoke head component 1) This gene encodes a male meiotic metaphase chromosome-associated acidic protein. This gene is expressed in tissues with motile cilia or flagella, including the trachea, lungs, airway brushings, and testes. Mutations in this gene result in primary ciliary dyskinesia-24. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2014]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BP6: Variant 21-42475587-T-C is Benign according to our data. Variant chr21-42475587-T-C is described in ClinVar as [Benign]. Clinvar id is 1250884.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.311 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RSPH1	NM_080860.4	c.877+311A>G		intron_variant		ENST00000291536.8	NP_543136.1
RSPH1	NM_001286506.2	c.763+311A>G		intron_variant			NP_001273435.1
RSPH1	XM_005261208.3	c.670+311A>G		intron_variant			XP_005261265.1
RSPH1	XM_011529786.2	c.805+311A>G		intron_variant			XP_011528088.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RSPH1	ENST00000291536.8	c.877+311A>G		intron_variant		1	NM_080860.4	ENSP00000291536	P1
RSPH1	ENST00000398352.3	c.763+311A>G		intron_variant		5		ENSP00000381395
RSPH1	ENST00000493019.1	n.2495+311A>G		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.219 AC: 30956 AN: 141320 Hom.: 3973 Cov.: 22

Gnomad AFR AF: 0.316

Gnomad AMI AF: 0.323

Gnomad AMR AF: 0.160

Gnomad ASJ AF: 0.196

Gnomad EAS AF: 0.00793

Gnomad SAS AF: 0.145

Gnomad FIN AF: 0.205

Gnomad MID AF: 0.173

Gnomad NFE AF: 0.200

Gnomad OTH AF: 0.180

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

GnomAD4 genome AF: 0.219 AC: 30985 AN: 141378 Hom.: 3976 Cov.: 22 AF XY: 0.215 AC XY: 14573 AN XY: 67896

Gnomad4 AFR AF: 0.316

Gnomad4 AMR AF: 0.160

Gnomad4 ASJ AF: 0.196

Gnomad4 EAS AF: 0.00796

Gnomad4 SAS AF: 0.145

Gnomad4 FIN AF: 0.205

Gnomad4 NFE AF: 0.200

Gnomad4 OTH AF: 0.181

Alfa AF: 0.00933 Hom.: 9

Bravo AF: 0.229

Asia WGS AF: 0.0710 AC: 240 AN: 3358

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

Dec 17, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.033
DANN	Benign	0.51

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: rs7275527; hg19: chr21-43895697;