X-101862596-C-A

Variant names:

• chrX-101862596-C-A
• rs17556

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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 the male GnomAd4 subpopulation. Median coverage is 23. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 6 gene

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.00468 AC: 524 AN: 111932 Hom.: 6 Cov.: 23

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

African (AFR) AF: 0.000877 AC: 27 AN: 30787

American (AMR) AF: 0.00407 AC: 43 AN: 10576

Ashkenazi Jewish (ASJ) AF: 0.0192 AC: 51 AN: 2650

East Asian (EAS) AF: 0.0403 AC: 143 AN: 3548

South Asian (SAS) AF: 0.0187 AC: 50 AN: 2674

European-Finnish (FIN) AF: 0.000494 AC: 3 AN: 6072

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 216

European-Non Finnish (NFE) AF: 0.00361 AC: 192 AN: 53249

Other (OTH) AF: 0.0111 AC: 17 AN: 1526

Alfa AF: 0.00136 Hom.: 6

Bravo AF: 0.00454

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	6.0
DANN	Benign	0.53
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs17556; hg19: chrX-101117568;