rs1016410

Positions:

• chr2-185786654-G-A

Variant summary

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

The NM_173651.4(FSIP2):​c.1506+366G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.314 in 151,644 control chromosomes in the GnomAD database, including 7,808 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 0.31 (7808 hom., cov: 31)
• Consequence: FSIP2 NM_173651.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.136

Genes affected

FSIP2 (HGNC:21675): (fibrous sheath interacting protein 2) This gene encodes a protein associated with the sperm fibrous sheath. Genes encoding most of the fibrous-sheath associated proteins genes are transcribed only during the postmeiotic period of spermatogenesis. The protein encoded by this gene is specific to spermatogenic cells. Copy number variation in this gene may be associated with testicular germ cell tumors. Pseudogenes associated with this gene are reported on chromosomes 2 and X. [provided by RefSeq, Aug 2016]

FSIP2-AS1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.371 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FSIP2	NM_173651.4	c.1506+366G>A		intron_variant		ENST00000424728.6	NP_775922.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FSIP2	ENST00000424728.6	c.1506+366G>A		intron_variant		5	NM_173651.4	ENSP00000401306.1
FSIP2-AS1	ENST00000436557.5	n.249+2112C>T		intron_variant		3
FSIP2-AS1	ENST00000667756.1	n.37+2112C>T		intron_variant

Frequencies

GnomAD3 genomes AF: 0.314 AC: 47640 AN: 151526 Hom.: 7810 Cov.: 31

Gnomad AFR AF: 0.245

Gnomad AMI AF: 0.286

Gnomad AMR AF: 0.380

Gnomad ASJ AF: 0.435

Gnomad EAS AF: 0.380

Gnomad SAS AF: 0.268

Gnomad FIN AF: 0.239

Gnomad MID AF: 0.417

Gnomad NFE AF: 0.345

Gnomad OTH AF: 0.348

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

GnomAD4 genome AF: 0.314 AC: 47629 AN: 151644 Hom.: 7808 Cov.: 31 AF XY: 0.309 AC XY: 22906 AN XY: 74106

Gnomad4 AFR AF: 0.244

Gnomad4 AMR AF: 0.380

Gnomad4 ASJ AF: 0.435

Gnomad4 EAS AF: 0.381

Gnomad4 SAS AF: 0.267

Gnomad4 FIN AF: 0.239

Gnomad4 NFE AF: 0.345

Gnomad4 OTH AF: 0.344

Alfa AF: 0.328 Hom.: 2915

Bravo AF: 0.324

Asia WGS AF: 0.298 AC: 1041 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	1.9
DANN	Benign	0.54

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: rs1016410; hg19: chr2-186651381;