15-68829384-A-G

Position:

• chr15-68829384-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000560188.1(SPESP1):​n.97+11067A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.936 in 152,172 control chromosomes in the GnomAD database, including 67,119 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.94 (67119 hom., cov: 30)
• Consequence: SPESP1 ENST00000560188.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.404

Genes affected

SPESP1 (HGNC:15570): (sperm equatorial segment protein 1) The encoded protein is a human alloantigen involved in sperm-egg binding and fusion. [provided by RefSeq, Apr 2010]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.979 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SPESP1	ENST00000560188.1	n.97+11067A>G		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.936 AC: 142381 AN: 152054 Hom.: 67073 Cov.: 30

Gnomad AFR AF: 0.818

Gnomad AMI AF: 0.977

Gnomad AMR AF: 0.975

Gnomad ASJ AF: 0.978

Gnomad EAS AF: 0.927

Gnomad SAS AF: 0.972

Gnomad FIN AF: 0.996

Gnomad MID AF: 0.946

Gnomad NFE AF: 0.985

Gnomad OTH AF: 0.962

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

GnomAD4 genome AF: 0.936 AC: 142482 AN: 152172 Hom.: 67119 Cov.: 30 AF XY: 0.938 AC XY: 69782 AN XY: 74382

Gnomad4 AFR AF: 0.818

Gnomad4 AMR AF: 0.975

Gnomad4 ASJ AF: 0.978

Gnomad4 EAS AF: 0.928

Gnomad4 SAS AF: 0.972

Gnomad4 FIN AF: 0.996

Gnomad4 NFE AF: 0.985

Gnomad4 OTH AF: 0.960

Alfa AF: 0.962 Hom.: 8229

Bravo AF: 0.929

Asia WGS AF: 0.937 AC: 3259 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.5
DANN	Benign	0.48

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1869476; hg19: chr15-69121723;