rs1019430

Variant names:

• chr2-185786784-C-T
• rs1019430
• NM_173651.4:c.1506+496C>T

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+496C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.545 in 151,456 control chromosomes in the GnomAD database, including 22,718 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 0.54 (22718 hom., cov: 31)
• Consequence: FSIP2 NM_173651.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.235
• Publications: 0 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=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.625 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+496C>T		intron	N/A	NP_775922.3
	FSIP2-AS1	NR_144453.1		n.249+1982G>A		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+496C>T		intron	N/A	ENSP00000401306.1
	FSIP2-AS1	ENST00000436557.5	TSL:3	n.249+1982G>A		intron	N/A
	FSIP2-AS1	ENST00000667756.2		n.247+1982G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.545 AC: 82422 AN: 151338 Hom.: 22686 Cov.: 31

Gnomad AFR AF: 0.559

Gnomad AMI AF: 0.609

Gnomad AMR AF: 0.496

Gnomad ASJ AF: 0.449

Gnomad EAS AF: 0.488

Gnomad SAS AF: 0.644

Gnomad FIN AF: 0.622

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.537

Gnomad OTH AF: 0.520

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

GnomAD4 genome AF: 0.545 AC: 82508 AN: 151456 Hom.: 22718 Cov.: 31 AF XY: 0.550 AC XY: 40737 AN XY: 74036

African (AFR) AF: 0.560 AC: 23150 AN: 41366

American (AMR) AF: 0.496 AC: 7518 AN: 15172

Ashkenazi Jewish (ASJ) AF: 0.449 AC: 1556 AN: 3462

East Asian (EAS) AF: 0.487 AC: 2493 AN: 5124

South Asian (SAS) AF: 0.644 AC: 3096 AN: 4806

European-Finnish (FIN) AF: 0.622 AC: 6558 AN: 10542

Middle Eastern (MID) AF: 0.449 AC: 132 AN: 294

European-Non Finnish (NFE) AF: 0.537 AC: 36356 AN: 67678

Other (OTH) AF: 0.521 AC: 1095 AN: 2102

Alfa AF: 0.545 Hom.: 2931

Bravo AF: 0.532

Asia WGS AF: 0.587 AC: 2038 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.7
DANN	Benign	0.66
PhyloP100		0.23
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: rs1019430; hg19: chr2-186651511;