rs12007101

Variant names:

• chrX-6539630-C-T
• rs12007101

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 0.166 in 110,556 control chromosomes in the GnomAD database, including 2,451 homozygotes. There are 5,131 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 0.17 (2451 hom., 5131 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.00
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.451 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: 0.166 AC: 18357 AN: 110503 Hom.: 2450 Cov.: 22

Gnomad AFR AF: 0.457

Gnomad AMI AF: 0.0235

Gnomad AMR AF: 0.0973

Gnomad ASJ AF: 0.0643

Gnomad EAS AF: 0.00143

Gnomad SAS AF: 0.0936

Gnomad FIN AF: 0.0230

Gnomad MID AF: 0.0932

Gnomad NFE AF: 0.0523

Gnomad OTH AF: 0.143

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

GnomAD4 genome AF: 0.166 AC: 18397 AN: 110556 Hom.: 2451 Cov.: 22 AF XY: 0.156 AC XY: 5131 AN XY: 32846

African (AFR) AF: 0.457 AC: 13818 AN: 30230

American (AMR) AF: 0.0973 AC: 1011 AN: 10393

Ashkenazi Jewish (ASJ) AF: 0.0643 AC: 169 AN: 2630

East Asian (EAS) AF: 0.00144 AC: 5 AN: 3479

South Asian (SAS) AF: 0.0928 AC: 242 AN: 2608

European-Finnish (FIN) AF: 0.0230 AC: 137 AN: 5957

Middle Eastern (MID) AF: 0.101 AC: 22 AN: 217

European-Non Finnish (NFE) AF: 0.0523 AC: 2763 AN: 52849

Other (OTH) AF: 0.142 AC: 214 AN: 1511

Alfa AF: 0.129 Hom.: 1620

Bravo AF: 0.185

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.14
DANN	Benign	0.12
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs12007101; hg19: chrX-6457671;