chrX-30101660-A-G

Variant names:

• chrX-30101660-A-G
• rs6628506

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 0.504 in 110,276 control chromosomes in the GnomAD database, including 10,484 homozygotes. There are 15,846 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 0.50 (10484 hom., 15846 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.18
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.547 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.504 AC: 55591 AN: 110219 Hom.: 10487 Cov.: 22

Gnomad AFR AF: 0.553

Gnomad AMI AF: 0.568

Gnomad AMR AF: 0.490

Gnomad ASJ AF: 0.478

Gnomad EAS AF: 0.0544

Gnomad SAS AF: 0.257

Gnomad FIN AF: 0.484

Gnomad MID AF: 0.528

Gnomad NFE AF: 0.525

Gnomad OTH AF: 0.495

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

GnomAD4 genome AF: 0.504 AC: 55631 AN: 110276 Hom.: 10484 Cov.: 22 AF XY: 0.487 AC XY: 15846 AN XY: 32554

African (AFR) AF: 0.554 AC: 16770 AN: 30291

American (AMR) AF: 0.490 AC: 5104 AN: 10418

Ashkenazi Jewish (ASJ) AF: 0.478 AC: 1257 AN: 2627

East Asian (EAS) AF: 0.0549 AC: 195 AN: 3554

South Asian (SAS) AF: 0.259 AC: 666 AN: 2572

European-Finnish (FIN) AF: 0.484 AC: 2828 AN: 5837

Middle Eastern (MID) AF: 0.528 AC: 112 AN: 212

European-Non Finnish (NFE) AF: 0.525 AC: 27592 AN: 52603

Other (OTH) AF: 0.487 AC: 731 AN: 1500

Alfa AF: 0.509 Hom.: 43713

Bravo AF: 0.510

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.56
DANN	Benign	0.34
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs6628506; hg19: chrX-30119777;