15-68828768-T-G

Variant names:

• chr15-68828768-T-G
• rs897001
• ENST00000560188.1:n.97+10451T>G

Variant summary

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

The ENST00000560188.1(SPESP1):​n.97+10451T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.936 in 152,280 control chromosomes in the GnomAD database, including 67,164 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 (67164 hom., cov: 33)
• Consequence: SPESP1 ENST00000560188.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.197

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=-0.61).
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SPESP1	ENST00000560188.1	n.97+10451T>G		intron_variant	Intron 1 of 1	2

Frequencies

GnomAD3 genomes AF: 0.936 AC: 142475 AN: 152162 Hom.: 67118 Cov.: 33

Gnomad AFR AF: 0.818

Gnomad AMI AF: 0.977

Gnomad AMR AF: 0.975

Gnomad ASJ AF: 0.978

Gnomad EAS AF: 0.928

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: 142576 AN: 152280 Hom.: 67164 Cov.: 33 AF XY: 0.938 AC XY: 69859 AN XY: 74464

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: 0.960 Hom.: 8723

Bravo AF: 0.929

Asia WGS AF: 0.937 AC: 3260 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.61
CADD	Benign	9.4
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs897001; hg19: chr15-69121107;