rs195677

Variant names:

• chrX-73871950-T-G
• rs195677

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 0.087 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.0869 AC: 9651 AN: 111006 Hom.: 359 Cov.: 22 AF XY: 0.0817 AC XY: 2714 AN XY: 33216

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

Gnomad4 AFR AF: 0.0612

Gnomad4 AMR AF: 0.0903

Gnomad4 ASJ AF: 0.0540

Gnomad4 EAS AF: 0.00762

Gnomad4 SAS AF: 0.0688

Gnomad4 FIN AF: 0.0930

Gnomad4 NFE AF: 0.110

Gnomad4 OTH AF: 0.0666

Alfa AF: 0.0982 Hom.: 635

Bravo AF: 0.0851

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs195677; hg19: chrX-73091785;