rs8033662

Variant names:

• chr15-68830375-G-A
• rs8033662
• ENST00000560188.1:n.97+12058G>A

Your query was ambiguous. Multiple possible variants found:

• chr15-68830375-G-A
• chr15-68830375-G-C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000560188.1(SPESP1):​n.97+12058G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.927 in 152,204 control chromosomes in the GnomAD database, including 65,916 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 0.93 (65916 hom., cov: 30)
• Consequence: SPESP1 ENST00000560188.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.73
• Publications: 3 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.978 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+12058G>A		intron_variant	Intron 1 of 1	2

Frequencies

GnomAD3 genomes AF: 0.927 AC: 140953 AN: 152086 Hom.: 65878 Cov.: 30

Gnomad AFR AF: 0.785

Gnomad AMI AF: 0.973

Gnomad AMR AF: 0.970

Gnomad ASJ AF: 0.978

Gnomad EAS AF: 0.928

Gnomad SAS AF: 0.972

Gnomad FIN AF: 0.996

Gnomad MID AF: 0.943

Gnomad NFE AF: 0.985

Gnomad OTH AF: 0.958

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

GnomAD4 genome AF: 0.927 AC: 141043 AN: 152204 Hom.: 65916 Cov.: 30 AF XY: 0.929 AC XY: 69121 AN XY: 74404

African (AFR) AF: 0.785 AC: 32578 AN: 41476

American (AMR) AF: 0.970 AC: 14842 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.978 AC: 3392 AN: 3470

East Asian (EAS) AF: 0.928 AC: 4796 AN: 5168

South Asian (SAS) AF: 0.972 AC: 4691 AN: 4826

European-Finnish (FIN) AF: 0.996 AC: 10572 AN: 10616

Middle Eastern (MID) AF: 0.942 AC: 277 AN: 294

European-Non Finnish (NFE) AF: 0.985 AC: 66987 AN: 68030

Other (OTH) AF: 0.956 AC: 2021 AN: 2114

Alfa AF: 0.930 Hom.: 10487

Bravo AF: 0.918

Asia WGS AF: 0.935 AC: 3252 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.16
DANN	Benign	0.59
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs8033662; hg19: chr15-69122714;