rs12007101

chrX-6539630-C-T

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 0.166 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.166 AC: 18357 AN: 110503 Hom.: 2450 Cov.: 22 AF XY: 0.155 AC XY: 5096 AN XY: 32785

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

Gnomad4 AFR AF: 0.457

Gnomad4 AMR AF: 0.0973

Gnomad4 ASJ AF: 0.0643

Gnomad4 EAS AF: 0.00144

Gnomad4 SAS AF: 0.0928

Gnomad4 FIN AF: 0.0230

Gnomad4 NFE AF: 0.0523

Gnomad4 OTH AF: 0.142

Alfa AF: 0.114 Hom.: 1330

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12007101; hg19: chrX-6457671;