chrX-51569739-G-A

Variant names:

• chrX-51569739-G-A
• rs5945645

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 0.0315 in 112,005 control chromosomes in the GnomAD database, including 72 homozygotes. There are 1,058 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 0.032 (72 hom., 1058 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.126
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0315 (3533/112005) while in subpopulation NFE AF = 0.0454 (2414/53203). AF 95% confidence interval is 0.0439. There are 72 homozygotes in GnomAd4. There are 1058 alleles in the male GnomAd4 subpopulation. Median coverage is 23. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 72 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: 0.0315 AC: 3531 AN: 111950 Hom.: 72 Cov.: 23

Gnomad AFR AF: 0.00597

Gnomad AMI AF: 0.225

Gnomad AMR AF: 0.0333

Gnomad ASJ AF: 0.0265

Gnomad EAS AF: 0.000281

Gnomad SAS AF: 0.0104

Gnomad FIN AF: 0.0446

Gnomad MID AF: 0.0169

Gnomad NFE AF: 0.0454

Gnomad OTH AF: 0.0378

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

GnomAD4 genome AF: 0.0315 AC: 3533 AN: 112005 Hom.: 72 Cov.: 23 AF XY: 0.0310 AC XY: 1058 AN XY: 34179

African (AFR) AF: 0.00595 AC: 184 AN: 30902

American (AMR) AF: 0.0333 AC: 350 AN: 10520

Ashkenazi Jewish (ASJ) AF: 0.0265 AC: 70 AN: 2639

East Asian (EAS) AF: 0.000282 AC: 1 AN: 3552

South Asian (SAS) AF: 0.0111 AC: 30 AN: 2698

European-Finnish (FIN) AF: 0.0446 AC: 271 AN: 6073

Middle Eastern (MID) AF: 0.0186 AC: 4 AN: 215

European-Non Finnish (NFE) AF: 0.0454 AC: 2414 AN: 53203

Other (OTH) AF: 0.0373 AC: 57 AN: 1527

Alfa AF: 0.0425 Hom.: 331

Bravo AF: 0.0315

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.074
DANN	Benign	0.14
PhyloP100		-0.13

Splicing

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

Other links and lift over

dbSNP: rs5945645; hg19: chrX-51312591;