rs752

Variant names:

• chrX-130470449-G-A
• rs752
• ENST00000612348.2:n.4101C>T

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

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

Genes affected

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

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000612348.2. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FSIP2LP	ENST00000612348.2	TSL:6	n.4101C>T		non_coding_transcript_exon	Exon 7 of 20

Frequencies

GnomAD3 genomes AF: 0.592 AC: 65160 AN: 110066 Hom.: 14512 Cov.: 22

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 1

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.785 AC: 23824 AN: 30338

American (AMR) AF: 0.667 AC: 6906 AN: 10349

Ashkenazi Jewish (ASJ) AF: 0.543 AC: 1414 AN: 2606

East Asian (EAS) AF: 0.872 AC: 3036 AN: 3482

South Asian (SAS) AF: 0.657 AC: 1693 AN: 2576

European-Finnish (FIN) AF: 0.538 AC: 3072 AN: 5708

Middle Eastern (MID) AF: 0.617 AC: 132 AN: 214

European-Non Finnish (NFE) AF: 0.453 AC: 23862 AN: 52669

Other (OTH) AF: 0.615 AC: 928 AN: 1510

Alfa AF: 0.530 Hom.: 3941

Bravo AF: 0.618

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.2
DANN	Benign	0.18
PhyloP100		0.48

Splicing

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

Other links and lift over

dbSNP: rs752; hg19: chrX-129604423;