rs7067102

Variant names:

• chrX-885339-A-G
• rs7067102

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 0.0781 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
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• 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

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

African (AFR) AF: 0.112 AC: 4656 AN: 41522

American (AMR) AF: 0.0655 AC: 1002 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0613 AC: 213 AN: 3472

East Asian (EAS) AF: 0.0228 AC: 118 AN: 5182

South Asian (SAS) AF: 0.123 AC: 594 AN: 4818

European-Finnish (FIN) AF: 0.0475 AC: 505 AN: 10624

Middle Eastern (MID) AF: 0.0918 AC: 27 AN: 294

European-Non Finnish (NFE) AF: 0.0669 AC: 4548 AN: 67998

Other (OTH) AF: 0.0848 AC: 179 AN: 2110

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
PhyloP100		-0.54

Splicing

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

Other links and lift over

dbSNP: rs7067102; hg19: chrX-846074;