X-55867932-T-C

Variant names:

• chrX-55867932-T-C
• rs1536163
• ENST00000799648.1:n.103-9782A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000799648.1(ENSG00000304092):​n.103-9782A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.515 in 110,125 control chromosomes in the GnomAD database, including 12,923 homozygotes. There are 16,840 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 0.51 (12923 hom., 16840 hem., cov: 22)
• Consequence: ENSG00000304092 ENST00000799648.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.284
• Publications: 3 publications found

Genes affected

ENSG00000304092 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.721 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
ENSG00000304092	ENST00000799648.1	n.103-9782A>G		intron_variant	Intron 1 of 2
ENSG00000304092	ENST00000799649.1	n.199-262A>G		intron_variant	Intron 1 of 4
ENSG00000304092	ENST00000799650.1	n.101-8443A>G		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.515 AC: 56686 AN: 110069 Hom.: 12931 Cov.: 22

Gnomad AFR AF: 0.114

Gnomad AMI AF: 0.870

Gnomad AMR AF: 0.475

Gnomad ASJ AF: 0.499

Gnomad EAS AF: 0.745

Gnomad SAS AF: 0.640

Gnomad FIN AF: 0.783

Gnomad MID AF: 0.349

Gnomad NFE AF: 0.703

Gnomad OTH AF: 0.466

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

GnomAD4 genome AF: 0.515 AC: 56664 AN: 110125 Hom.: 12923 Cov.: 22 AF XY: 0.520 AC XY: 16840 AN XY: 32377

African (AFR) AF: 0.113 AC: 3455 AN: 30506

American (AMR) AF: 0.475 AC: 4899 AN: 10317

Ashkenazi Jewish (ASJ) AF: 0.499 AC: 1310 AN: 2626

East Asian (EAS) AF: 0.745 AC: 2592 AN: 3478

South Asian (SAS) AF: 0.641 AC: 1620 AN: 2526

European-Finnish (FIN) AF: 0.783 AC: 4405 AN: 5624

Middle Eastern (MID) AF: 0.354 AC: 75 AN: 212

European-Non Finnish (NFE) AF: 0.703 AC: 37024 AN: 52648

Other (OTH) AF: 0.460 AC: 695 AN: 1511

Alfa AF: 0.591 Hom.: 22457

Bravo AF: 0.476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	3.9
DANN	Benign	0.80
PhyloP100		0.28

Splicing

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

Other links and lift over

dbSNP: rs1536163; hg19: chrX-55894365;