X-38875477-T-C

Variant names:

• chrX-38875477-T-C
• rs199871
• ENST00000687892.1:n.76+4633T>C

Variant summary

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

The ENST00000687892.1(ENSG00000289127):​n.76+4633T>C variant causes a intron 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 0.40 (6555 hom., 11670 hem., cov: 20)
• Consequence: ENSG00000289127 ENST00000687892.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.27

Genes affected

ENSG00000289127 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.06).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.508 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124905177	XR_007068213.1	n.98+4633T>C		intron_variant	Intron 1 of 1
LOC124905177	XR_007068214.1	n.98+4633T>C		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000289127	ENST00000687892.1	n.76+4633T>C		intron_variant	Intron 1 of 1
ENSG00000289127	ENST00000688782.1	n.78+4633T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.404 AC: 43276 AN: 107180 Hom.: 6557 Cov.: 20 AF XY: 0.390 AC XY: 11664 AN XY: 29930

Gnomad AFR AF: 0.441

Gnomad AMI AF: 0.218

Gnomad AMR AF: 0.476

Gnomad ASJ AF: 0.294

Gnomad EAS AF: 0.507

Gnomad SAS AF: 0.533

Gnomad FIN AF: 0.357

Gnomad MID AF: 0.352

Gnomad NFE AF: 0.370

Gnomad OTH AF: 0.377

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

GnomAD4 genome AF: 0.404 AC: 43271 AN: 107208 Hom.: 6555 Cov.: 20 AF XY: 0.389 AC XY: 11670 AN XY: 29968

Gnomad4 AFR AF: 0.440

Gnomad4 AMR AF: 0.475

Gnomad4 ASJ AF: 0.294

Gnomad4 EAS AF: 0.507

Gnomad4 SAS AF: 0.532

Gnomad4 FIN AF: 0.357

Gnomad4 NFE AF: 0.370

Gnomad4 OTH AF: 0.379

Alfa AF: 0.277 Hom.: 1472

Bravo AF: 0.421

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.81
DANN	Benign	0.25

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs199871; hg19: chrX-38734730;