rs4658635

chr1-244366101-A-Gchr1-244366101-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.56+1345A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.784 in 152,042 control chromosomes in the GnomAD database, including 46,898 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 0.78 (46898 hom., cov: 31)
• Consequence: C1orf100 NM_001012970.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0870

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=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.901 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
C1orf100	NM_001012970.3	c.56+1345A>G		intron_variant		ENST00000308105.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SPMIP3	ENST00000308105.5	c.56+1345A>G		intron_variant		2	NM_001012970.3	P1
SPMIP3	ENST00000366537.5	c.56+1345A>G		intron_variant		1
SPMIP3	ENST00000486803.1	n.155+1345A>G		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.784 AC: 119103 AN: 151924 Hom.: 46855 Cov.: 31

Gnomad AFR AF: 0.789

Gnomad AMI AF: 0.700

Gnomad AMR AF: 0.833

Gnomad ASJ AF: 0.642

Gnomad EAS AF: 0.923

Gnomad SAS AF: 0.832

Gnomad FIN AF: 0.798

Gnomad MID AF: 0.778

Gnomad NFE AF: 0.762

Gnomad OTH AF: 0.798

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

GnomAD4 genome AF: 0.784 AC: 119205 AN: 152042 Hom.: 46898 Cov.: 31 AF XY: 0.790 AC XY: 58675 AN XY: 74296

Gnomad4 AFR AF: 0.789

Gnomad4 AMR AF: 0.833

Gnomad4 ASJ AF: 0.642

Gnomad4 EAS AF: 0.923

Gnomad4 SAS AF: 0.831

Gnomad4 FIN AF: 0.798

Gnomad4 NFE AF: 0.762

Gnomad4 OTH AF: 0.800

Alfa AF: 0.762 Hom.: 25636

Bravo AF: 0.787

Asia WGS AF: 0.892 AC: 3099 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	1.3
Dann	Benign	0.26

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: rs4658635; hg19: chr1-244529403;