rs12007229

Variant names:

• chrX-67528513-C-A
• rs12007229

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 0.11 in 110,387 control chromosomes in the GnomAD database, including 658 homozygotes. There are 3,211 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 0.11 (658 hom., 3211 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.426
• Publications: 15 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.203 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: 0.110 AC: 12147 AN: 110335 Hom.: 658 Cov.: 22

Gnomad AFR AF: 0.208

Gnomad AMI AF: 0.0192

Gnomad AMR AF: 0.0742

Gnomad ASJ AF: 0.0629

Gnomad EAS AF: 0.000575

Gnomad SAS AF: 0.0250

Gnomad FIN AF: 0.0533

Gnomad MID AF: 0.116

Gnomad NFE AF: 0.0822

Gnomad OTH AF: 0.127

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

GnomAD4 genome AF: 0.110 AC: 12154 AN: 110387 Hom.: 658 Cov.: 22 AF XY: 0.0982 AC XY: 3211 AN XY: 32711

African (AFR) AF: 0.208 AC: 6277 AN: 30235

American (AMR) AF: 0.0741 AC: 769 AN: 10371

Ashkenazi Jewish (ASJ) AF: 0.0629 AC: 165 AN: 2625

East Asian (EAS) AF: 0.000576 AC: 2 AN: 3470

South Asian (SAS) AF: 0.0239 AC: 62 AN: 2591

European-Finnish (FIN) AF: 0.0533 AC: 318 AN: 5962

Middle Eastern (MID) AF: 0.118 AC: 25 AN: 212

European-Non Finnish (NFE) AF: 0.0822 AC: 4334 AN: 52746

Other (OTH) AF: 0.126 AC: 189 AN: 1499

Alfa AF: 0.0847 Hom.: 2366

Bravo AF: 0.116

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.6
DANN	Benign	0.80
PhyloP100		-0.43

Splicing

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

Other links and lift over

dbSNP: rs12007229; hg19: chrX-66748355;