X-15624289-G-C

Variant names:

• chrX-15624289-G-C
• rs1356037
• ENST00000649243.1:n.356+15273C>G

Variant summary

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

The ENST00000649243.1(ENSG00000285602):​n.356+15273C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.3 in 110,868 control chromosomes in the GnomAD database, including 3,623 homozygotes. There are 9,849 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 0.30 (3623 hom., 9849 hem., cov: 23)
• Consequence: ENSG00000285602 ENST00000649243.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.930

Genes affected

ENSG00000285602 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.415 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000285602	ENST00000649243.1	n.356+15273C>G		intron_variant	Intron 5 of 19			ENSP00000497489.1

Frequencies

GnomAD3 genomes AF: 0.300 AC: 33215 AN: 110815 Hom.: 3619 Cov.: 23 AF XY: 0.297 AC XY: 9841 AN XY: 33085

Gnomad AFR AF: 0.309

Gnomad AMI AF: 0.306

Gnomad AMR AF: 0.295

Gnomad ASJ AF: 0.234

Gnomad EAS AF: 0.432

Gnomad SAS AF: 0.225

Gnomad FIN AF: 0.337

Gnomad MID AF: 0.239

Gnomad NFE AF: 0.290

Gnomad OTH AF: 0.314

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

GnomAD4 genome AF: 0.300 AC: 33236 AN: 110868 Hom.: 3623 Cov.: 23 AF XY: 0.297 AC XY: 9849 AN XY: 33148

Gnomad4 AFR AF: 0.308

Gnomad4 AMR AF: 0.295

Gnomad4 ASJ AF: 0.234

Gnomad4 EAS AF: 0.433

Gnomad4 SAS AF: 0.224

Gnomad4 FIN AF: 0.337

Gnomad4 NFE AF: 0.290

Gnomad4 OTH AF: 0.317

Alfa AF: 0.105 Hom.: 455

Bravo AF: 0.304

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.9
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1356037; hg19: chrX-15642412;