chrX-42357911-G-A

Variant names:

• chrX-42357911-G-A
• rs17310225
• ENST00000411879.5:n.194-64554G>A

Variant summary

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

The ENST00000411879.5(ENSG00000231772):​n.194-64554G>A 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 0.14 (863 hom., 4141 hem., cov: 20)
• Consequence: ENSG00000231772 ENST00000411879.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.367
• Publications: 1 publications found

Genes affected

ENSG00000231772 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.16 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
ENSG00000231772	ENST00000411879.5	n.194-64554G>A		intron_variant	Intron 2 of 7	5

Frequencies

GnomAD3 genomes AF: 0.143 AC: 15606 AN: 109084 Hom.: 862 Cov.: 20

Gnomad AFR AF: 0.165

Gnomad AMI AF: 0.0396

Gnomad AMR AF: 0.116

Gnomad ASJ AF: 0.152

Gnomad EAS AF: 0.130

Gnomad SAS AF: 0.0969

Gnomad FIN AF: 0.122

Gnomad MID AF: 0.124

Gnomad NFE AF: 0.142

Gnomad OTH AF: 0.147

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

GnomAD4 genome AF: 0.143 AC: 15611 AN: 109126 Hom.: 863 Cov.: 20 AF XY: 0.132 AC XY: 4141 AN XY: 31454

African (AFR) AF: 0.164 AC: 4916 AN: 29915

American (AMR) AF: 0.116 AC: 1174 AN: 10130

Ashkenazi Jewish (ASJ) AF: 0.152 AC: 399 AN: 2628

East Asian (EAS) AF: 0.130 AC: 450 AN: 3456

South Asian (SAS) AF: 0.0972 AC: 244 AN: 2510

European-Finnish (FIN) AF: 0.122 AC: 680 AN: 5557

Middle Eastern (MID) AF: 0.123 AC: 26 AN: 212

European-Non Finnish (NFE) AF: 0.142 AC: 7473 AN: 52573

Other (OTH) AF: 0.152 AC: 222 AN: 1464

Alfa AF: 0.143 Hom.: 3889

Bravo AF: 0.146

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.69
DANN	Benign	0.74
PhyloP100		-0.37

Splicing

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

Other links and lift over

dbSNP: rs17310225; hg19: chrX-42217163;