dbSNP rs115898419: SPEF2:c.2840-13G>A (chr5-35712799-G-A) – ACMG Classification: Benign (-18 pts)

Variant summary

Our verdict is Benign. Variant got -18 ACMG points: 0P and 18B. BP4_ModerateBP6_Very_StrongBA1

The NM_024867.4(SPEF2):c.2840-13G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0224 in 1,612,932 control chromosomes in the GnomAD database, including 714 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.019 ( 64 hom., cov: 34)

Exomes 𝑓: 0.023 ( 650 hom. )

Consequence

SPEF2
NM_024867.4 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: 0.362

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:

ENSG00000248969 (HGNC:):

ENSG00000248969 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -18 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.26).

BP6

Variant 5-35712799-G-A is Benign according to our data. Variant chr5-35712799-G-A is described in ClinVar as [Benign]. Clinvar id is 403480.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAdExome4 highest subpopulation (MID) allele frequency at 95% confidence interval = 0.0818 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SPEF2	NM_024867.4 link	c.2840-13G>A		intron_variant	Intron 19 of 36	ENST00000356031.8	NP_079143.3	Q9C093-1A0A140VKD0

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
SPEF2	ENST00000356031.8 link	c.2840-13G>A	intron_variant	Intron 19 of 36	1	NM_024867.4	ENSP00000348314.3	Q9C093-1
SPEF2	ENST00000637569.1 link	c.2840-13G>A	intron_variant	Intron 19 of 34	5		ENSP00000490886.1	A0A1B0GWD8
SPEF2	ENST00000440995.6 link	c.2825-13G>A	intron_variant	Intron 19 of 36	5		ENSP00000412125.2	Q9C093-2
ENSG00000248969	ENST00000510433.1 link	n.174-14764C>T	intron_variant	Intron 1 of 3	4

Frequencies

GnomAD3 genomes

AF:

0.0187

AC:

2850

AN:

152120

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00302

Gnomad AMI

AF:

0.00877

Gnomad AMR

AF:

0.0180

Gnomad ASJ

AF:

0.0757

Gnomad EAS

AF:

0.00443

Gnomad SAS

AF:

0.0535

Gnomad FIN

AF:

0.0317

Gnomad MID

AF:

0.0316

Gnomad NFE

AF:

0.0221

Gnomad OTH

AF:

0.0244

GnomAD3 exomes

AF:

0.0271

AC:

6727

AN:

248304

Hom.:

158

AF XY:

0.0299

AC XY:

4034

AN XY:

134730

show subpopulations

Gnomad AFR exome

AF:

0.00208

Gnomad AMR exome

AF:

0.0130

Gnomad ASJ exome

AF:

0.0854

Gnomad EAS exome

AF:

0.00490

Gnomad SAS exome

AF:

0.0596

Gnomad FIN exome

AF:

0.0334

Gnomad NFE exome

AF:

0.0227

Gnomad OTH exome

AF:

0.0361

GnomAD4 exome

AF:

0.0228

AC:

33331

AN:

1460694

Hom.:

650

Cov.:

AF XY:

0.0246

AC XY:

17852

AN XY:

726606

show subpopulations

Gnomad4 AFR exome

AF:

0.00380

Gnomad4 AMR exome

AF:

0.0132

Gnomad4 ASJ exome

AF:

0.0853

Gnomad4 EAS exome

AF:

0.00280

Gnomad4 SAS exome

AF:

0.0618

Gnomad4 FIN exome

AF:

0.0328

Gnomad4 NFE exome

AF:

0.0189

Gnomad4 OTH exome

AF:

0.0281

GnomAD4 genome

AF:

0.0188

AC:

2856

AN:

152238

Hom.:

Cov.:

AF XY:

0.0202

AC XY:

1502

AN XY:

74444

show subpopulations

Gnomad4 AFR

AF:

0.00303

Gnomad4 AMR

AF:

0.0179

Gnomad4 ASJ

AF:

0.0757

Gnomad4 EAS

AF:

0.00444

Gnomad4 SAS

AF:

0.0539

Gnomad4 FIN

AF:

0.0317

Gnomad4 NFE

AF:

0.0221

Gnomad4 OTH

AF:

0.0255

Alfa

AF:

0.0319

Hom.:

Bravo

AF:

0.0168

Asia WGS

AF:

0.0250

AC:

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

May 05, 2021

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

not specified

Benign:1

Mar 29, 2016

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.26

CADD

Benign

DANN

Benign

0.80

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