rs12008633

Variant names:

• chrX-40543027-G-T
• rs12008633

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 0.192 in 111,029 control chromosomes in the GnomAD database, including 1,778 homozygotes. There are 6,192 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 0.19 (1778 hom., 6192 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.401
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.69).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.322 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: 0.192 AC: 21272 AN: 110974 Hom.: 1777 Cov.: 22

Gnomad AFR AF: 0.327

Gnomad AMI AF: 0.119

Gnomad AMR AF: 0.161

Gnomad ASJ AF: 0.0918

Gnomad EAS AF: 0.0359

Gnomad SAS AF: 0.117

Gnomad FIN AF: 0.257

Gnomad MID AF: 0.0975

Gnomad NFE AF: 0.134

Gnomad OTH AF: 0.170

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

GnomAD4 genome AF: 0.192 AC: 21290 AN: 111029 Hom.: 1778 Cov.: 22 AF XY: 0.186 AC XY: 6192 AN XY: 33281

African (AFR) AF: 0.327 AC: 9960 AN: 30425

American (AMR) AF: 0.161 AC: 1691 AN: 10504

Ashkenazi Jewish (ASJ) AF: 0.0918 AC: 242 AN: 2636

East Asian (EAS) AF: 0.0358 AC: 127 AN: 3550

South Asian (SAS) AF: 0.117 AC: 317 AN: 2700

European-Finnish (FIN) AF: 0.257 AC: 1496 AN: 5830

Middle Eastern (MID) AF: 0.0930 AC: 20 AN: 215

European-Non Finnish (NFE) AF: 0.134 AC: 7104 AN: 52978

Other (OTH) AF: 0.167 AC: 252 AN: 1509

Alfa AF: 0.157 Hom.: 11103

Bravo AF: 0.197

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
CADD	Benign	3.5
DANN	Benign	0.85
PhyloP100		-0.40

Splicing

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

Other links and lift over

dbSNP: rs12008633; hg19: chrX-40402279;