rs1016410

Variant names:

• chr2-185786654-G-A
• rs1016410
• NM_173651.4:c.1506+366G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

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:40978): (FSIP2 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_173651.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FSIP2	NM_173651.4	MANE Select	c.1506+366G>A		intron	N/A	NP_775922.3
	FSIP2-AS1	NR_144453.1		n.249+2112C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FSIP2	ENST00000424728.6	TSL:5 MANE Select	c.1506+366G>A		intron	N/A	ENSP00000401306.1
	FSIP2-AS1	ENST00000436557.5	TSL:3	n.249+2112C>T		intron	N/A
	FSIP2-AS1	ENST00000667756.2		n.247+2112C>T		intron	N/A

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

African (AFR) AF: 0.244 AC: 10113 AN: 41394

American (AMR) AF: 0.380 AC: 5773 AN: 15210

Ashkenazi Jewish (ASJ) AF: 0.435 AC: 1507 AN: 3468

East Asian (EAS) AF: 0.381 AC: 1955 AN: 5128

South Asian (SAS) AF: 0.267 AC: 1286 AN: 4808

European-Finnish (FIN) AF: 0.239 AC: 2529 AN: 10584

Middle Eastern (MID) AF: 0.414 AC: 120 AN: 290

European-Non Finnish (NFE) AF: 0.345 AC: 23360 AN: 67742

Other (OTH) AF: 0.344 AC: 725 AN: 2108

Alfa AF: 0.329 Hom.: 3285

Bravo AF: 0.324

Asia WGS AF: 0.298 AC: 1041 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	1.9
DANN	Benign	0.54
PhyloP100		0.14
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1016410; hg19: chr2-186651381;