rs7067102

Variant names:

• chrX-885339-A-G
• rs7067102

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 0.0781 in 152,228 control chromosomes in the GnomAD database, including 538 homozygotes. There are 5,740 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 0.078 (538 hom., 5740 hem., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.537

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.115 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: 0.0779 AC: 11854 AN: 152110 Hom.: 531 Cov.: 32 AF XY: 0.0769 AC XY: 5713 AN XY: 74304

Gnomad AFR AF: 0.112

Gnomad AMI AF: 0.0482

Gnomad AMR AF: 0.0655

Gnomad ASJ AF: 0.0613

Gnomad EAS AF: 0.0223

Gnomad SAS AF: 0.124

Gnomad FIN AF: 0.0475

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0669

Gnomad OTH AF: 0.0843

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

GnomAD4 genome AF: 0.0781 AC: 11886 AN: 152228 Hom.: 538 Cov.: 32 AF XY: 0.0771 AC XY: 5740 AN XY: 74432

Gnomad4 AFR AF: 0.112

Gnomad4 AMR AF: 0.0655

Gnomad4 ASJ AF: 0.0613

Gnomad4 EAS AF: 0.0228

Gnomad4 SAS AF: 0.123

Gnomad4 FIN AF: 0.0475

Gnomad4 NFE AF: 0.0669

Gnomad4 OTH AF: 0.0848

Bravo AF: 0.0794

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.2
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7067102; hg19: chrX-846074;