rs17407

Variant names:

• chrX-141994899-A-G
• rs17407
• ENST00000664519.1:n.222+60182A>G

Variant summary

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

The ENST00000664519.1(ENSG00000288098):​n.222+60182A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.32 in 111,425 control chromosomes in the GnomAD database, including 4,702 homozygotes. There are 9,933 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 0.32 (4702 hom., 9933 hem., cov: 23)
• Consequence: ENSG00000288098 ENST00000664519.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.55

Genes affected

ENSG00000288098 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.388 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
ENSG00000288098	ENST00000664519.1	n.222+60182A>G		intron_variant	Intron 1 of 9

Frequencies

GnomAD3 genomes AF: 0.320 AC: 35628 AN: 111370 Hom.: 4699 Cov.: 23 AF XY: 0.295 AC XY: 9924 AN XY: 33602

Gnomad AFR AF: 0.270

Gnomad AMI AF: 0.356

Gnomad AMR AF: 0.251

Gnomad ASJ AF: 0.533

Gnomad EAS AF: 0.00167

Gnomad SAS AF: 0.116

Gnomad FIN AF: 0.233

Gnomad MID AF: 0.432

Gnomad NFE AF: 0.392

Gnomad OTH AF: 0.334

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

GnomAD4 genome AF: 0.320 AC: 35643 AN: 111425 Hom.: 4702 Cov.: 23 AF XY: 0.295 AC XY: 9933 AN XY: 33667

Gnomad4 AFR AF: 0.270

Gnomad4 AMR AF: 0.250

Gnomad4 ASJ AF: 0.533

Gnomad4 EAS AF: 0.00168

Gnomad4 SAS AF: 0.117

Gnomad4 FIN AF: 0.233

Gnomad4 NFE AF: 0.392

Gnomad4 OTH AF: 0.330

Alfa AF: 0.371 Hom.: 21688

Bravo AF: 0.319

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.089
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17407; hg19: chrX-141082685;