X-100075518-A-G

Variant names:

• chrX-100075518-A-G
• rs985251

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.51 in 110,274 control chromosomes in the GnomAD database, including 12,615 homozygotes. There are 16,758 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 0.51 (12615 hom., 16758 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.94
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.56).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.683 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.510 AC: 56207 AN: 110222 Hom.: 12620 Cov.: 22

Gnomad AFR AF: 0.109

Gnomad AMI AF: 0.853

Gnomad AMR AF: 0.574

Gnomad ASJ AF: 0.570

Gnomad EAS AF: 0.523

Gnomad SAS AF: 0.611

Gnomad FIN AF: 0.773

Gnomad MID AF: 0.458

Gnomad NFE AF: 0.689

Gnomad OTH AF: 0.514

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

GnomAD4 genome AF: 0.510 AC: 56208 AN: 110274 Hom.: 12615 Cov.: 22 AF XY: 0.513 AC XY: 16758 AN XY: 32660

African (AFR) AF: 0.109 AC: 3343 AN: 30644

American (AMR) AF: 0.574 AC: 5883 AN: 10255

Ashkenazi Jewish (ASJ) AF: 0.570 AC: 1493 AN: 2618

East Asian (EAS) AF: 0.524 AC: 1808 AN: 3452

South Asian (SAS) AF: 0.611 AC: 1573 AN: 2576

European-Finnish (FIN) AF: 0.773 AC: 4467 AN: 5779

Middle Eastern (MID) AF: 0.449 AC: 97 AN: 216

European-Non Finnish (NFE) AF: 0.689 AC: 36186 AN: 52553

Other (OTH) AF: 0.519 AC: 780 AN: 1503

Alfa AF: 0.577 Hom.: 6332

Bravo AF: 0.484

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.56
CADD	Benign	15
DANN	Benign	0.78
PhyloP100		1.9

Splicing

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

Other links and lift over

dbSNP: rs985251; hg19: chrX-99330516;