X-27114257-T-C

Position:

• chrX-27114257-T-C

Variant summary

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

The ENST00000609836.1(ENSG00000242021):​n.89+44648A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.442 in 110,369 control chromosomes in the GnomAD database, including 7,814 homozygotes. There are 14,432 hemizygotes in GnomAD. 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 0.44 (7814 hom., 14432 hem., cov: 23)
• Consequence: ENSG00000242021 ENST00000609836.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.304

Genes affected

ENSG00000242021 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.671 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
ENSG00000242021	ENST00000609836.1	n.89+44648A>G		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.442 AC: 48779 AN: 110318 Hom.: 7817 Cov.: 23 AF XY: 0.442 AC XY: 14411 AN XY: 32568

Gnomad AFR AF: 0.335

Gnomad AMI AF: 0.641

Gnomad AMR AF: 0.472

Gnomad ASJ AF: 0.458

Gnomad EAS AF: 0.695

Gnomad SAS AF: 0.551

Gnomad FIN AF: 0.479

Gnomad MID AF: 0.416

Gnomad NFE AF: 0.469

Gnomad OTH AF: 0.433

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

GnomAD4 genome AF: 0.442 AC: 48791 AN: 110369 Hom.: 7814 Cov.: 23 AF XY: 0.442 AC XY: 14432 AN XY: 32629

Gnomad4 AFR AF: 0.335

Gnomad4 AMR AF: 0.473

Gnomad4 ASJ AF: 0.458

Gnomad4 EAS AF: 0.694

Gnomad4 SAS AF: 0.552

Gnomad4 FIN AF: 0.479

Gnomad4 NFE AF: 0.469

Gnomad4 OTH AF: 0.434

Alfa AF: 0.466 Hom.: 20254

Bravo AF: 0.440

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.6
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1037193; hg19: chrX-27132374;