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chrY-624389-T-G

Position:

• chrY-624389-T-G

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_Strong BP6_Moderate

The ENST00000711145.1(SHOX):​c.-646T>G variant causes a 5 prime UTR premature start codon gain change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency: Genomes: not found (cov:)
• Consequence: SHOX ENST00000711145.1 5_prime_UTR_premature_start_codon_gain
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.252

Genes affected

SHOX (HGNC:10853): (SHOX homeobox) This gene belongs to the paired homeobox family and is located in the pseudoautosomal region 1 (PAR1) of X and Y chromosomes. Defects in this gene are associated with idiopathic growth retardation and in the short stature phenotype of Turner syndrome patients. This gene is highly conserved across species from mammals to fish to flies. Alternatively spliced transcript variants encoding different isoforms have been noted for this gene. [provided by RefSeq, Jul 2008]

SHOX_1 (HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -6 ACMG points.

• BP4: Computational evidence support a benign effect (Cadd=1.215).
• BP6: Variant Y-624389-T-G is Benign according to our data. Variant chrY-624389-T-G is described in ClinVar as [Likely_benign]. Clinvar id is 2659855.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SHOX_1	NM_006883.2_1	c.-646T>G		5_prime_UTR_premature_start_codon_gain_variant	1/6
SHOX_1	NM_006883.2_1	c.-646T>G		5_prime_UTR_variant	1/6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SHOX	ENST00000711145.1	c.-646T>G		5_prime_UTR_premature_start_codon_gain_variant	1/6	5		ENSP00000518642.1
SHOX	ENST00000711143.1	c.-646T>G		5_prime_UTR_premature_start_codon_gain_variant	1/6	5		ENSP00000518641.1
SHOX	ENST00000711145.1	c.-646T>G		5_prime_UTR_variant	1/6	5		ENSP00000518642.1
SHOX	ENST00000711143.1	c.-646T>G		5_prime_UTR_variant	1/6	5		ENSP00000518641.1

Frequencies

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

We have no GnomAD4 genomes data on this position. Probably position not covered by the project.

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Dec 01, 2022

SHOX: BS2 -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
CADD	Benign	1.2

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs950355194; hg19: chrY-535124;