rs17556

Positions:

• chrX-101862596-C-A
• chrX-101862596-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.0047 in 111,984 control chromosomes in the GnomAD database, including 6 homozygotes. There are 150 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 0.0047 (6 hom., 150 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.26

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BS1: Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.0047 (526/111984) while in subpopulation EAS AF= 0.0403 (143/3548). AF 95% confidence interval is 0.0349. There are 6 homozygotes in gnomad4. There are 150 alleles in male gnomad4 subpopulation. Median coverage is 23. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 6 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.00468 AC: 524 AN: 111932 Hom.: 6 Cov.: 23 AF XY: 0.00434 AC XY: 148 AN XY: 34078

Gnomad AFR AF: 0.000879

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00407

Gnomad ASJ AF: 0.0192

Gnomad EAS AF: 0.0402

Gnomad SAS AF: 0.0183

Gnomad FIN AF: 0.000494

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00361

Gnomad OTH AF: 0.0106

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

GnomAD4 genome AF: 0.00470 AC: 526 AN: 111984 Hom.: 6 Cov.: 23 AF XY: 0.00439 AC XY: 150 AN XY: 34140

Gnomad4 AFR AF: 0.000877

Gnomad4 AMR AF: 0.00407

Gnomad4 ASJ AF: 0.0192

Gnomad4 EAS AF: 0.0403

Gnomad4 SAS AF: 0.0187

Gnomad4 FIN AF: 0.000494

Gnomad4 NFE AF: 0.00361

Gnomad4 OTH AF: 0.0111

Alfa AF: 0.00136 Hom.: 6

Bravo AF: 0.00454

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	6.0
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17556; hg19: chrX-101117568;