2-185738694-C-T

Variant names:

• chr2-185738694-C-T
• rs778782758
• ENST00000421998.6:n.28G>A

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 0P and 2B. BP4_Moderate

The ENST00000421998.6(FSIP2-AS1):​n.28G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000108 in 1,383,730 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.000011 (0 hom.)
• Consequence: FSIP2-AS1 ENST00000421998.6 non_coding_transcript_exon
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: -0.282
• Publications: 0 publications found

Genes affected

FSIP2-AS1 (HGNC:40978): (FSIP2 antisense RNA 1)

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-AS2 (HGNC:54061): (FSIP2 antisense RNA 2)

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• BP4: Computational evidence support a benign effect (REVEL=0.041).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000421998.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FSIP2-AS2	NR_110215.1		n.26G>A		non_coding_transcript_exon	Exon 1 of 4
	FSIP2-AS2	NR_110216.1		n.26G>A		non_coding_transcript_exon	Exon 1 of 4
	FSIP2-AS2	NR_110214.1		n.187+213G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FSIP2-AS1	ENST00000421998.6	TSL:1	n.28G>A		non_coding_transcript_exon	Exon 1 of 4
	FSIP2-AS1	ENST00000769859.1		n.292G>A		non_coding_transcript_exon	Exon 1 of 4
	FSIP2-AS1	ENST00000769860.1		n.49G>A		non_coding_transcript_exon	Exon 1 of 4

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD2 exomes AF: 0.0000688 AC: 9 AN: 130740 AF XY: 0.0000562

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.0000203

Gnomad OTH exome AF: 0.00197

GnomAD4 exome AF: 0.0000108 AC: 15 AN: 1383730 Hom.: 0 Cov.: 31 AF XY: 0.0000103 AC XY: 7 AN XY: 682818

African (AFR) AF: 0.00 AC: 0 AN: 31594

American (AMR) AF: 0.00 AC: 0 AN: 35700

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 25178

East Asian (EAS) AF: 0.00 AC: 0 AN: 35732

South Asian (SAS) AF: 0.00 AC: 0 AN: 79234

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 33846

Middle Eastern (MID) AF: 0.00211 AC: 12 AN: 5694

European-Non Finnish (NFE) AF: 9.27e-7 AC: 1 AN: 1078850

Other (OTH) AF: 0.0000345 AC: 2 AN: 57902

GnomAD4 genome Cov.: 32

Alfa AF: 0.000508 Hom.: 0

ClinVar

ClinVar submissions as Germline

Significance: Uncertain significance

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	1	-	not specified (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.63
CADD	Benign	5.4
DANN	Benign	0.87
PhyloP100		-0.28
PromoterAI		-0.056	Neutral

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: rs778782758; hg19: chr2-186603421;