X-87747441-A-G

Position:

• chrX-87747441-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000635331.1(ENSG00000282914):​n.129+3314T>C variant causes a intron, non coding transcript 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 0.31 (6168 hom., 7800 hem., cov: 20)
• Consequence: ENST00000635331.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.23

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.662 is higher than 0.05.

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
	ENST00000635331.1	n.129+3314T>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.307 AC: 32473 AN: 105905 Hom.: 6160 Cov.: 20 AF XY: 0.267 AC XY: 7771 AN XY: 29145

Gnomad AFR AF: 0.669

Gnomad AMI AF: 0.199

Gnomad AMR AF: 0.296

Gnomad ASJ AF: 0.190

Gnomad EAS AF: 0.543

Gnomad SAS AF: 0.244

Gnomad FIN AF: 0.0906

Gnomad MID AF: 0.145

Gnomad NFE AF: 0.131

Gnomad OTH AF: 0.280

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

GnomAD4 genome AF: 0.307 AC: 32513 AN: 105922 Hom.: 6168 Cov.: 20 AF XY: 0.267 AC XY: 7800 AN XY: 29176

Gnomad4 AFR AF: 0.670

Gnomad4 AMR AF: 0.297

Gnomad4 ASJ AF: 0.190

Gnomad4 EAS AF: 0.543

Gnomad4 SAS AF: 0.244

Gnomad4 FIN AF: 0.0906

Gnomad4 NFE AF: 0.131

Gnomad4 OTH AF: 0.276

Alfa AF: 0.192 Hom.: 3358

Bravo AF: 0.358

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.71
DANN	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5924105; hg19: chrX-87002441;