NM_001320752.2:c.-207A>C

Variant names:

• chrX-7148010-A-C
• rs1473666
• NM_001320752.2:c.-207A>C

Variant summary

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

The NM_001320752.2(STS):​c.-207A>C variant causes a 5 prime UTR 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 0.68 (18532 hom., 21106 hem., cov: 21)
  • Exomes 𝑓: 0.61 (124680 hom. 180816 hem.)
  • Failed GnomAD Quality Control
• Consequence: STS NM_001320752.2 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0340
• Publications: 8 publications found

Genes affected

STS (HGNC:11425): (steroid sulfatase) This gene encodes a multi-pass membrane protein that is localized to the endoplasmic reticulum. It belongs to the sulfatase family and hydrolyzes several 3-beta-hydroxysteroid sulfates, which serve as metabolic precursors for estrogens, androgens, and cholesterol. Mutations in this gene are associated with X-linked ichthyosis (XLI). Alternatively spliced transcript variants resulting from the use of different promoters have been described for this gene (PMID:17601726). [provided by RefSeq, Mar 2016]

PUDP (HGNC:16818): (pseudouridine 5'-phosphatase) This gene encodes a member of the haloacid dehalogenase-like (HAD) hydrolase superfamily. The encoded protein has no known biological function. This gene has a pseudogene on chromosome 1. Multiple alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Jul 2010]

MIR4767 (HGNC:41548): (microRNA 4767) microRNAs (miRNAs) are short (20-24 nt) non-coding RNAs that are involved in post-transcriptional regulation of gene expression in multicellular organisms by affecting both the stability and translation of mRNAs. miRNAs are transcribed by RNA polymerase II as part of capped and polyadenylated primary transcripts (pri-miRNAs) that can be either protein-coding or non-coding. The primary transcript is cleaved by the Drosha ribonuclease III enzyme to produce an approximately 70-nt stem-loop precursor miRNA (pre-miRNA), which is further cleaved by the cytoplasmic Dicer ribonuclease to generate the mature miRNA and antisense miRNA star (miRNA*) products. The mature miRNA is incorporated into a RNA-induced silencing complex (RISC), which recognizes target mRNAs through imperfect base pairing with the miRNA and most commonly results in translational inhibition or destabilization of the target mRNA. The RefSeq represents the predicted microRNA stem-loop. [provided by RefSeq, Sep 2009]

ACMG classification

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

• BP4: Computational evidence support a benign effect (REVEL=0.045).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
STS	NM_001320752.2	c.-207A>C		5_prime_UTR_variant	Exon 1 of 11	ENST00000674429.1	NP_001307681.2
PUDP	NM_012080.5	c.61+43T>G		intron_variant	Intron 1 of 3	ENST00000381077.10	NP_036212.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
STS	ENST00000674429.1	c.-207A>C		5_prime_UTR_variant	Exon 1 of 11		NM_001320752.2	ENSP00000501534.1
PUDP	ENST00000381077.10	c.61+43T>G		intron_variant	Intron 1 of 3	1	NM_012080.5	ENSP00000370467.6

Frequencies

GnomAD3 genomes AF: 0.677 AC: 73652 AN: 108741 Hom.: 18530 Cov.: 21

Gnomad AFR AF: 0.868

Gnomad AMI AF: 0.365

Gnomad AMR AF: 0.669

Gnomad ASJ AF: 0.634

Gnomad EAS AF: 0.593

Gnomad SAS AF: 0.753

Gnomad FIN AF: 0.537

Gnomad MID AF: 0.632

Gnomad NFE AF: 0.592

Gnomad OTH AF: 0.654

GnomAD2 exomes AF: 0.624 AC: 54692 AN: 87580 AF XY: 0.635

Gnomad AFR exome AF: 0.878

Gnomad AMR exome AF: 0.636

Gnomad ASJ exome AF: 0.626

Gnomad EAS exome AF: 0.559

Gnomad FIN exome AF: 0.548

Gnomad NFE exome AF: 0.583

Gnomad OTH exome AF: 0.628

GnomAD4 exome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.609 AC: 588589 AN: 966760 Hom.: 124680 Cov.: 17 AF XY: 0.622 AC XY: 180816 AN XY: 290862

African (AFR) AF: 0.878 AC: 18245 AN: 20777

American (AMR) AF: 0.643 AC: 15939 AN: 24804

Ashkenazi Jewish (ASJ) AF: 0.634 AC: 10850 AN: 17127

East Asian (EAS) AF: 0.645 AC: 14868 AN: 23056

South Asian (SAS) AF: 0.758 AC: 35218 AN: 46435

European-Finnish (FIN) AF: 0.546 AC: 20112 AN: 36843

Middle Eastern (MID) AF: 0.673 AC: 2572 AN: 3822

European-Non Finnish (NFE) AF: 0.592 AC: 445568 AN: 753055

Other (OTH) AF: 0.617 AC: 25217 AN: 40841

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.678 AC: 73702 AN: 108781 Hom.: 18532 Cov.: 21 AF XY: 0.672 AC XY: 21106 AN XY: 31409

African (AFR) AF: 0.868 AC: 26114 AN: 30084

American (AMR) AF: 0.669 AC: 7024 AN: 10493

Ashkenazi Jewish (ASJ) AF: 0.634 AC: 1652 AN: 2604

East Asian (EAS) AF: 0.592 AC: 1984 AN: 3350

South Asian (SAS) AF: 0.754 AC: 1928 AN: 2558

European-Finnish (FIN) AF: 0.537 AC: 2908 AN: 5417

Middle Eastern (MID) AF: 0.641 AC: 134 AN: 209

European-Non Finnish (NFE) AF: 0.592 AC: 30756 AN: 51931

Other (OTH) AF: 0.650 AC: 964 AN: 1483

Alfa AF: 0.641 Hom.: 17342

Bravo AF: 0.690

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	9.0
DANN	Benign	0.30
PhyloP100		0.034
PromoterAI		-0.056	Neutral
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: rs1473666; hg19: chrX-7066051; COSMIC: COSV66903752; COSMIC: COSV66903752;