rs3102458

chr1-244376566-A-Gchr1-244376566-A-T

Variant summary

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

The NM_001012970.3(C1orf100):c.152+1099A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.211 in 152,026 control chromosomes in the GnomAD database, including 3,509 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 0.21 (3509 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: C1orf100 NM_001012970.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.67

Genes affected

C1orf100 (HGNC:):

SPMIP3 (HGNC:30435): (sperm microtubule inner protein 3)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.264 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
C1orf100	NM_001012970.3	c.152+1099A>G		intron_variant		ENST00000308105.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SPMIP3	ENST00000308105.5	c.152+1099A>G		intron_variant		2	NM_001012970.3	P1
SPMIP3	ENST00000366537.5	c.152+1099A>G		intron_variant		1
	ENST00000417765.1	n.158-103T>C		intron_variant, non_coding_transcript_variant		3
SPMIP3	ENST00000486803.1	n.251+1099A>G		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.211 AC: 32075 AN: 151908 Hom.: 3505 Cov.: 32

Gnomad AFR AF: 0.170

Gnomad AMI AF: 0.369

Gnomad AMR AF: 0.230

Gnomad ASJ AF: 0.254

Gnomad EAS AF: 0.185

Gnomad SAS AF: 0.275

Gnomad FIN AF: 0.241

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.219

Gnomad OTH AF: 0.236

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

GnomAD4 genome AF: 0.211 AC: 32099 AN: 152026 Hom.: 3509 Cov.: 32 AF XY: 0.213 AC XY: 15848 AN XY: 74324

Gnomad4 AFR AF: 0.170

Gnomad4 AMR AF: 0.230

Gnomad4 ASJ AF: 0.254

Gnomad4 EAS AF: 0.185

Gnomad4 SAS AF: 0.276

Gnomad4 FIN AF: 0.241

Gnomad4 NFE AF: 0.219

Gnomad4 OTH AF: 0.240

Alfa AF: 0.213 Hom.: 5254

Bravo AF: 0.207

Asia WGS AF: 0.213 AC: 739 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	7.3
Dann	Benign	0.61

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: rs3102458; hg19: chr1-244539868;