rs3101457

Positions:

• chr1-244369912-G-A
• chr1-244369912-G-C

Variant summary

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

The NM_001012970.3(C1orf100):​c.56+5156G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.802 in 152,032 control chromosomes in the GnomAD database, including 49,108 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 0.80 (49108 hom., cov: 31)
• Consequence: C1orf100 NM_001012970.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.08

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 (SAS) allele frequency at 95% confidence interval = 0.907 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
C1orf100	NM_001012970.3	c.56+5156G>A		intron_variant		ENST00000308105.5	NP_001012988.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SPMIP3	ENST00000308105.5	c.56+5156G>A		intron_variant		2	NM_001012970.3	ENSP00000311218	P1
SPMIP3	ENST00000366537.5	c.56+5156G>A		intron_variant		1		ENSP00000355495
SPMIP3	ENST00000486803.1	n.155+5156G>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.802 AC: 121762 AN: 151916 Hom.: 49060 Cov.: 31

Gnomad AFR AF: 0.732

Gnomad AMI AF: 0.816

Gnomad AMR AF: 0.859

Gnomad ASJ AF: 0.832

Gnomad EAS AF: 0.919

Gnomad SAS AF: 0.930

Gnomad FIN AF: 0.793

Gnomad MID AF: 0.782

Gnomad NFE AF: 0.812

Gnomad OTH AF: 0.827

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

GnomAD4 genome AF: 0.802 AC: 121864 AN: 152032 Hom.: 49108 Cov.: 31 AF XY: 0.805 AC XY: 59791 AN XY: 74290

Gnomad4 AFR AF: 0.732

Gnomad4 AMR AF: 0.859

Gnomad4 ASJ AF: 0.832

Gnomad4 EAS AF: 0.919

Gnomad4 SAS AF: 0.929

Gnomad4 FIN AF: 0.793

Gnomad4 NFE AF: 0.812

Gnomad4 OTH AF: 0.830

Alfa AF: 0.810 Hom.: 57772

Bravo AF: 0.803

Asia WGS AF: 0.922 AC: 3206 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	0.76
DANN	Benign	0.31

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: rs3101457; hg19: chr1-244533214;