rs17219044

Variant names:

• chrX-4322642-A-C
• rs17219044

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 0.0101 in 110,603 control chromosomes in the GnomAD database, including 6 homozygotes. There are 300 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 0.010 (6 hom., 300 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.330
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0101 (1112/110603) while in subpopulation NFE AF = 0.0164 (866/52939). AF 95% confidence interval is 0.0155. There are 6 homozygotes in GnomAd4. There are 300 alleles in the male GnomAd4 subpopulation. Median coverage is 22. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 6 gene

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

Frequencies

GnomAD3 genomes AF: 0.0101 AC: 1112 AN: 110552 Hom.: 6 Cov.: 22

Gnomad AFR AF: 0.00192

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0106

Gnomad ASJ AF: 0.00837

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000781

Gnomad FIN AF: 0.00639

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0164

Gnomad OTH AF: 0.0107

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

GnomAD4 genome AF: 0.0101 AC: 1112 AN: 110603 Hom.: 6 Cov.: 22 AF XY: 0.00910 AC XY: 300 AN XY: 32979

African (AFR) AF: 0.00192 AC: 58 AN: 30221

American (AMR) AF: 0.0106 AC: 110 AN: 10411

Ashkenazi Jewish (ASJ) AF: 0.00837 AC: 22 AN: 2627

East Asian (EAS) AF: 0.00 AC: 0 AN: 3497

South Asian (SAS) AF: 0.000783 AC: 2 AN: 2553

European-Finnish (FIN) AF: 0.00639 AC: 38 AN: 5946

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 214

European-Non Finnish (NFE) AF: 0.0164 AC: 866 AN: 52939

Other (OTH) AF: 0.0106 AC: 16 AN: 1513

Alfa AF: 0.0123 Hom.: 74

Bravo AF: 0.00994

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.8
DANN	Benign	0.59
PhyloP100		0.33

Splicing

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

Other links and lift over

dbSNP: rs17219044; hg19: chrX-4240683; COSMIC: COSV58358100;