rs1056169851

Variant names:

• chrX-21856280-C-A
• NM_206923.4:c.-205C>A

Your query was ambiguous. Multiple possible variants found:

• chrX-21856280-C-A
• chrX-21856280-C-G
• chrX-21856280-C-T

Variant summary

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

The NM_206923.4(YY2):​c.-205C>A 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: not found (cov: 17)
  • Exomes 𝑓: 0.0000047 (0 hom. 0 hem.)
• Consequence: YY2 NM_206923.4 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.227

Genes affected

YY2 (HGNC:31684): (YY2 transcription factor) The protein encoded by this gene is a transcription factor that includes several Kruppel-like zinc fingers in its C-terminal region. It possesses both activation and repression domains, and it can therefore have both positive and negative effects on the transcription of target genes. This gene has an intronless coding region, and it appears to have arisen by retrotransposition of the related YY1 transcription factor gene, which is located on chromosome 14. [provided by RefSeq, May 2010]

MBTPS2 (HGNC:15455): (membrane bound transcription factor peptidase, site 2) This gene encodes a intramembrane zinc metalloprotease, which is essential in development. This protease functions in the signal protein activation involved in sterol control of transcription and the ER stress response. Mutations in this gene have been associated with ichthyosis follicularis with atrichia and photophobia (IFAP syndrome); IFAP syndrome has been quantitatively linked to a reduction in cholesterol homeostasis and ER stress response.[provided by RefSeq, Aug 2009]

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
YY2	NM_206923.4	c.-205C>A		5_prime_UTR_variant	Exon 1 of 1	ENST00000429584.3	NP_996806.2
MBTPS2	NM_015884.4	c.670+2777C>A		intron_variant	Intron 5 of 10	ENST00000379484.10	NP_056968.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
YY2	ENST00000429584	c.-205C>A		5_prime_UTR_variant	Exon 1 of 1		NM_206923.4	ENSP00000389381.2
MBTPS2	ENST00000379484.10	c.670+2777C>A		intron_variant	Intron 5 of 10	1	NM_015884.4	ENSP00000368798.5
MBTPS2	ENST00000365779.2	c.670+2777C>A		intron_variant	Intron 5 of 6	1		ENSP00000368796.1
MBTPS2	ENST00000465888.1	n.770-221C>A		intron_variant	Intron 5 of 5	2

Frequencies

GnomAD3 genomes Cov.: 17

GnomAD4 exome AF: 0.00000471 AC: 1 AN: 212092 Hom.: 0 Cov.: 3 AF XY: 0.00 AC XY: 0 AN XY: 73690

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00000721

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 17

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	1.4
DANN	Benign	0.78

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.030		Details are displayed if max score is > 0.2

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chrX-21874398;