rs752

Positions:

• chrX-130470449-G-A
• chrX-130470449-G-T

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000612348.2(FSIP2LP):​n.4101C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. 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 0.59 (14518 hom., 19359 hem., cov: 22)
  • Exomes 𝑓: 0.0 (0 hom. 0 hem.)
  • Failed GnomAD Quality Control
• Consequence: FSIP2LP ENST00000612348.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.481

Genes affected

FSIP2LP (HGNC:55625): (fibrous sheath interacting protein 2 like, pseudogene)

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FSIP2LP	ENST00000612348.2	n.4101C>T		non_coding_transcript_exon_variant	7/20

Frequencies

GnomAD3 genomes AF: 0.592 AC: 65160 AN: 110066 Hom.: 14512 Cov.: 22 AF XY: 0.597 AC XY: 19307 AN XY: 32332

Gnomad AFR AF: 0.785

Gnomad AMI AF: 0.523

Gnomad AMR AF: 0.667

Gnomad ASJ AF: 0.543

Gnomad EAS AF: 0.872

Gnomad SAS AF: 0.657

Gnomad FIN AF: 0.538

Gnomad MID AF: 0.630

Gnomad NFE AF: 0.453

Gnomad OTH AF: 0.612

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 1 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 1

Gnomad4 NFE exome AF: 0.00

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.592 AC: 65215 AN: 110117 Hom.: 14518 Cov.: 22 AF XY: 0.598 AC XY: 19359 AN XY: 32393

Gnomad4 AFR AF: 0.785

Gnomad4 AMR AF: 0.667

Gnomad4 ASJ AF: 0.543

Gnomad4 EAS AF: 0.872

Gnomad4 SAS AF: 0.657

Gnomad4 FIN AF: 0.538

Gnomad4 NFE AF: 0.453

Gnomad4 OTH AF: 0.615

Alfa AF: 0.530 Hom.: 3941

Bravo AF: 0.618

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.2
DANN	Benign	0.18

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs752; hg19: chrX-129604423;