rs3123710

chr1-244381516-G-Achr1-244381516-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.325+2877G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.571 in 152,096 control chromosomes in the GnomAD database, including 25,293 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 0.57 (25293 hom., cov: 33)
• Consequence: C1orf100 NM_001012970.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.13

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=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.64 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
C1orf100	NM_001012970.3	c.325+2877G>A		intron_variant		ENST00000308105.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SPMIP3	ENST00000308105.5	c.325+2877G>A		intron_variant		2	NM_001012970.3	P1
	ENST00000417765.1	n.158-5053C>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.571 AC: 86825 AN: 151978 Hom.: 25266 Cov.: 33

Gnomad AFR AF: 0.596

Gnomad AMI AF: 0.689

Gnomad AMR AF: 0.570

Gnomad ASJ AF: 0.622

Gnomad EAS AF: 0.255

Gnomad SAS AF: 0.658

Gnomad FIN AF: 0.555

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.574

Gnomad OTH AF: 0.535

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

GnomAD4 genome AF: 0.571 AC: 86900 AN: 152096 Hom.: 25293 Cov.: 33 AF XY: 0.569 AC XY: 42284 AN XY: 74342

Gnomad4 AFR AF: 0.596

Gnomad4 AMR AF: 0.570

Gnomad4 ASJ AF: 0.622

Gnomad4 EAS AF: 0.255

Gnomad4 SAS AF: 0.659

Gnomad4 FIN AF: 0.555

Gnomad4 NFE AF: 0.574

Gnomad4 OTH AF: 0.535

Alfa AF: 0.572 Hom.: 34722

Bravo AF: 0.567

Asia WGS AF: 0.459 AC: 1596 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	0.0030
Dann	Benign	0.41

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: rs3123710; hg19: chr1-244544818;