rs760867

Variant names:

• chrX-66160441-T-C
• rs760867

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 0.326 in 111,123 control chromosomes in the GnomAD database, including 8,092 homozygotes. There are 10,212 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 0.33 (8092 hom., 10212 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.830
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.809 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: 0.326 AC: 36155 AN: 111071 Hom.: 8085 Cov.: 23

Gnomad AFR AF: 0.817

Gnomad AMI AF: 0.134

Gnomad AMR AF: 0.219

Gnomad ASJ AF: 0.185

Gnomad EAS AF: 0.000851

Gnomad SAS AF: 0.0902

Gnomad FIN AF: 0.123

Gnomad MID AF: 0.172

Gnomad NFE AF: 0.134

Gnomad OTH AF: 0.267

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

GnomAD4 genome AF: 0.326 AC: 36221 AN: 111123 Hom.: 8092 Cov.: 23 AF XY: 0.306 AC XY: 10212 AN XY: 33393

African (AFR) AF: 0.818 AC: 24817 AN: 30354

American (AMR) AF: 0.219 AC: 2306 AN: 10541

Ashkenazi Jewish (ASJ) AF: 0.185 AC: 489 AN: 2639

East Asian (EAS) AF: 0.000853 AC: 3 AN: 3516

South Asian (SAS) AF: 0.0908 AC: 244 AN: 2687

European-Finnish (FIN) AF: 0.123 AC: 738 AN: 6003

Middle Eastern (MID) AF: 0.183 AC: 40 AN: 218

European-Non Finnish (NFE) AF: 0.134 AC: 7089 AN: 52964

Other (OTH) AF: 0.266 AC: 404 AN: 1520

Alfa AF: 0.224 Hom.: 7479

Bravo AF: 0.355

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.31
DANN	Benign	0.58
PhyloP100		-0.83

Splicing

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

Other links and lift over

dbSNP: rs760867; hg19: chrX-65380283;