5-35628718-A-G

Variant summary

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

The NM_024867.4(SPEF2):c.161+156A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.117 in 151,990 control chromosomes in the GnomAD database, including 2,332 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.12 (2332 hom., cov: 32)
• Consequence: SPEF2 NM_024867.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.652

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]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BP6: Variant 5-35628718-A-G is Benign according to our data. Variant chr5-35628718-A-G is described in ClinVar as [Benign]. Clinvar id is 1282434.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.321 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SPEF2	NM_024867.4	c.161+156A>G		intron_variant		ENST00000356031.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SPEF2	ENST00000356031.8	c.161+156A>G		intron_variant		1	NM_024867.4	P2

Frequencies

GnomAD3 genomes AF: 0.117 AC: 17777 AN: 151872 Hom.: 2318 Cov.: 32

Gnomad AFR AF: 0.325

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.0564

Gnomad ASJ AF: 0.0286

Gnomad EAS AF: 0.00154

Gnomad SAS AF: 0.0315

Gnomad FIN AF: 0.0592

Gnomad MID AF: 0.0637

Gnomad NFE AF: 0.0355

Gnomad OTH AF: 0.0910

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

GnomAD4 genome AF: 0.117 AC: 17849 AN: 151990 Hom.: 2332 Cov.: 32 AF XY: 0.114 AC XY: 8496 AN XY: 74306

Gnomad4 AFR AF: 0.326

Gnomad4 AMR AF: 0.0563

Gnomad4 ASJ AF: 0.0286

Gnomad4 EAS AF: 0.00155

Gnomad4 SAS AF: 0.0307

Gnomad4 FIN AF: 0.0592

Gnomad4 NFE AF: 0.0355

Gnomad4 OTH AF: 0.0938

Alfa AF: 0.0841 Hom.: 171

Bravo AF: 0.127

Asia WGS AF: 0.0520 AC: 179 AN: 3478

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

May 17, 2021

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	1.2
Dann	Benign	0.44

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: rs430828; hg19: chr5-35628820;