chrX-73871950-T-G

Variant names:

• chrX-73871950-T-G
• rs195677

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 0.087 in 111,054 control chromosomes in the GnomAD database, including 359 homozygotes. There are 2,719 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 0.087 (359 hom., 2719 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.187
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.107 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.0869 AC: 9651 AN: 111006 Hom.: 359 Cov.: 22

Gnomad AFR AF: 0.0613

Gnomad AMI AF: 0.0488

Gnomad AMR AF: 0.0898

Gnomad ASJ AF: 0.0540

Gnomad EAS AF: 0.00759

Gnomad SAS AF: 0.0686

Gnomad FIN AF: 0.0930

Gnomad MID AF: 0.0340

Gnomad NFE AF: 0.110

Gnomad OTH AF: 0.0667

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

GnomAD4 genome AF: 0.0870 AC: 9658 AN: 111054 Hom.: 359 Cov.: 22 AF XY: 0.0817 AC XY: 2719 AN XY: 33274

African (AFR) AF: 0.0612 AC: 1874 AN: 30636

American (AMR) AF: 0.0903 AC: 932 AN: 10323

Ashkenazi Jewish (ASJ) AF: 0.0540 AC: 143 AN: 2648

East Asian (EAS) AF: 0.00762 AC: 27 AN: 3543

South Asian (SAS) AF: 0.0688 AC: 182 AN: 2644

European-Finnish (FIN) AF: 0.0930 AC: 550 AN: 5913

Middle Eastern (MID) AF: 0.0376 AC: 8 AN: 213

European-Non Finnish (NFE) AF: 0.110 AC: 5808 AN: 52941

Other (OTH) AF: 0.0666 AC: 101 AN: 1517

Alfa AF: 0.0982 Hom.: 635

Bravo AF: 0.0851

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.1
DANN	Benign	0.45
PhyloP100		0.19

Splicing

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

Other links and lift over

dbSNP: rs195677; hg19: chrX-73091785;