rs1019430

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FSIP2	NM_173651.4	c.1506+496C>T		intron_variant	Intron 15 of 22	ENST00000424728.6	NP_775922.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FSIP2	ENST00000424728.6	c.1506+496C>T		intron_variant	Intron 15 of 22	5	NM_173651.4	ENSP00000401306.1
FSIP2-AS1	ENST00000436557.5	n.249+1982G>A		intron_variant	Intron 2 of 2	3
FSIP2-AS1	ENST00000667756.1	n.37+1982G>A		intron_variant	Intron 1 of 1

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

Gnomad4 AFR AF: 0.560

Gnomad4 AMR AF: 0.496

Gnomad4 ASJ AF: 0.449

Gnomad4 EAS AF: 0.487

Gnomad4 SAS AF: 0.644

Gnomad4 FIN AF: 0.622

Gnomad4 NFE AF: 0.537

Gnomad4 OTH AF: 0.521

Alfa AF: 0.545 Hom.: 2815

Bravo AF: 0.532

Asia WGS AF: 0.587 AC: 2038 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.7
DANN	Benign	0.66

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: rs1019430; hg19: chr2-186651511;