Variant chr5-35641717-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_024867.4(SPEF2):c.414+34C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00856 in 1,584,410 control chromosomes in the GnomAD database, including 323 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.0086 ( 33 hom., cov: 32)

Exomes 𝑓: 0.0086 ( 290 hom. )

Consequence

SPEF2
NM_024867.4 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.387

Variant links:

Genes affected

SPEF2 (HGNC:26293): (sperm flagellar 2) Involved in sperm axoneme assembly. Located in sperm flagellum. Implicated in spermatogenic failure 43. [provided by Alliance of Genome Resources, Apr 2022]

SPEF2 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.87).

BP6

Variant 5-35641717-C-T is Benign according to our data. Variant chr5-35641717-C-T is described in ClinVar as [Benign]. Clinvar id is 1181542.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0944 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SPEF2	NM_024867.4 linkuse as main transcript	c.414+34C>T		intron_variant		ENST00000356031.8	NP_079143.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SPEF2	ENST00000356031.8 linkuse as main transcript	c.414+34C>T		intron_variant		1	NM_024867.4	ENSP00000348314	P2	Q9C093-1

Frequencies

GnomAD3 genomes

AF:

0.00862

AC:

1311

AN:

152080

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00109

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00930

Gnomad ASJ

AF:

0.000288

Gnomad EAS

AF:

0.102

Gnomad SAS

AF:

0.0259

Gnomad FIN

AF:

0.0125

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00481

Gnomad OTH

AF:

0.00574

GnomAD3 exomes

AF:

0.0175

AC:

3979

AN:

226902

Hom.:

118

AF XY:

0.0177

AC XY:

2171

AN XY:

122974

show subpopulations

Gnomad AFR exome

AF:

0.00139

Gnomad AMR exome

AF:

0.0184

Gnomad ASJ exome

AF:

0.00205

Gnomad EAS exome

AF:

0.0969

Gnomad SAS exome

AF:

0.0331

Gnomad FIN exome

AF:

0.0116

Gnomad NFE exome

AF:

0.00556

Gnomad OTH exome

AF:

0.00915

GnomAD4 exome

AF:

0.00856

AC:

12255

AN:

1432212

Hom.:

290

Cov.:

AF XY:

0.00922

AC XY:

6555

AN XY:

710900

show subpopulations

Gnomad4 AFR exome

AF:

0.000782

Gnomad4 AMR exome

AF:

0.0187

Gnomad4 ASJ exome

AF:

0.00142

Gnomad4 EAS exome

AF:

0.0916

Gnomad4 SAS exome

AF:

0.0329

Gnomad4 FIN exome

AF:

0.0111

Gnomad4 NFE exome

AF:

0.00364

Gnomad4 OTH exome

AF:

0.00968

GnomAD4 genome

AF:

0.00859

AC:

1308

AN:

152198

Hom.:

Cov.:

AF XY:

0.00992

AC XY:

738

AN XY:

74412

show subpopulations

Gnomad4 AFR

AF:

0.00108

Gnomad4 AMR

AF:

0.00928

Gnomad4 ASJ

AF:

0.000288

Gnomad4 EAS

AF:

0.102

Gnomad4 SAS

AF:

0.0253

Gnomad4 FIN

AF:

0.0125

Gnomad4 NFE

AF:

0.00481

Gnomad4 OTH

AF:

0.00615

Alfa

AF:

0.00754

Hom.:

Bravo

AF:

0.00787

Asia WGS

AF:

0.0450

AC:

155

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	May 26, 2021	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

1.9

DANN

Benign

0.34

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