chrX-100075518-A-G

Variant names:

• chrX-100075518-A-G
• rs985251

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.510 AC: 56207 AN: 110222 Hom.: 12620 Cov.: 22 AF XY: 0.514 AC XY: 16745 AN XY: 32598

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

Gnomad4 AFR AF: 0.109

Gnomad4 AMR AF: 0.574

Gnomad4 ASJ AF: 0.570

Gnomad4 EAS AF: 0.524

Gnomad4 SAS AF: 0.611

Gnomad4 FIN AF: 0.773

Gnomad4 NFE AF: 0.689

Gnomad4 OTH AF: 0.519

Alfa AF: 0.577 Hom.: 6332

Bravo AF: 0.484

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs985251; hg19: chrX-99330516;