Variant chr5-35644234-T-G 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_024867.4(SPEF2):c.415-121T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.567 in 808,450 control chromosomes in the GnomAD database, including 133,198 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.60 ( 27589 hom., cov: 32)

Exomes 𝑓: 0.56 ( 105609 hom. )

Consequence

SPEF2
NM_024867.4 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.341

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:

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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=-0.86).

BP6

Variant 5-35644234-T-G is Benign according to our data. Variant chr5-35644234-T-G is described in ClinVar as [Benign]. Clinvar id is 1221024.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.718 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SPEF2	NM_024867.4 linkuse as main transcript	c.415-121T>G		intron_variant		ENST00000356031.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SPEF2	ENST00000356031.8 linkuse as main transcript	c.415-121T>G		intron_variant		1	NM_024867.4	P2	Q9C093-1

Frequencies

GnomAD3 genomes

AF:

0.596

AC:

90474

AN:

151790

Hom.:

27547

Cov.:

show subpopulations

Gnomad AFR

AF:

0.679

Gnomad AMI

AF:

0.479

Gnomad AMR

AF:

0.646

Gnomad ASJ

AF:

0.573

Gnomad EAS

AF:

0.738

Gnomad SAS

AF:

0.675

Gnomad FIN

AF:

0.471

Gnomad MID

AF:

0.542

Gnomad NFE

AF:

0.541

Gnomad OTH

AF:

0.584

GnomAD4 exome

AF:

0.561

AC:

368194

AN:

656542

Hom.:

105609

AF XY:

0.563

AC XY:

185026

AN XY:

328782

show subpopulations

Gnomad4 AFR exome

AF:

0.684

Gnomad4 AMR exome

AF:

0.679

Gnomad4 ASJ exome

AF:

0.565

Gnomad4 EAS exome

AF:

0.771

Gnomad4 SAS exome

AF:

0.656

Gnomad4 FIN exome

AF:

0.494

Gnomad4 NFE exome

AF:

0.539

Gnomad4 OTH exome

AF:

0.576

GnomAD4 genome

AF:

0.596

AC:

90580

AN:

151908

Hom.:

27589

Cov.:

AF XY:

0.595

AC XY:

44189

AN XY:

74244

show subpopulations

Gnomad4 AFR

AF:

0.680

Gnomad4 AMR

AF:

0.647

Gnomad4 ASJ

AF:

0.573

Gnomad4 EAS

AF:

0.737

Gnomad4 SAS

AF:

0.675

Gnomad4 FIN

AF:

0.471

Gnomad4 NFE

AF:

0.541

Gnomad4 OTH

AF:

0.582

Alfa

AF:

0.405

Hom.:

989

Bravo

AF:

0.613

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

May 15, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

5.4

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