rs17310225

chrX-42357911-G-A

Variant summary

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

The ENST00000411879.5(ENSG00000231772):n.194-64554G>A variant causes a intron, non coding transcript 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: ENST00000411879.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.367

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000411879.5	n.194-64554G>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.143 AC: 15606 AN: 109084 Hom.: 862 Cov.: 20 AF XY: 0.132 AC XY: 4140 AN XY: 31402

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

Gnomad4 AFR AF: 0.164

Gnomad4 AMR AF: 0.116

Gnomad4 ASJ AF: 0.152

Gnomad4 EAS AF: 0.130

Gnomad4 SAS AF: 0.0972

Gnomad4 FIN AF: 0.122

Gnomad4 NFE AF: 0.142

Gnomad4 OTH AF: 0.152

Alfa AF: 0.144 Hom.: 2570

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17310225; hg19: chrX-42217163;