X-67506664-A-G

Variant names:

• chrX-67506664-A-G
• rs6525177

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 0.343 in 110,194 control chromosomes in the GnomAD database, including 8,955 homozygotes. There are 10,257 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 0.34 (8955 hom., 10257 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.41
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.853 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: 0.343 AC: 37771 AN: 110143 Hom.: 8946 Cov.: 23

Gnomad AFR AF: 0.861

Gnomad AMI AF: 0.115

Gnomad AMR AF: 0.166

Gnomad ASJ AF: 0.115

Gnomad EAS AF: 0.00170

Gnomad SAS AF: 0.0811

Gnomad FIN AF: 0.114

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.160

Gnomad OTH AF: 0.295

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

GnomAD4 genome AF: 0.343 AC: 37833 AN: 110194 Hom.: 8955 Cov.: 23 AF XY: 0.315 AC XY: 10257 AN XY: 32516

African (AFR) AF: 0.861 AC: 25965 AN: 30144

American (AMR) AF: 0.166 AC: 1713 AN: 10329

Ashkenazi Jewish (ASJ) AF: 0.115 AC: 301 AN: 2627

East Asian (EAS) AF: 0.00170 AC: 6 AN: 3527

South Asian (SAS) AF: 0.0806 AC: 212 AN: 2631

European-Finnish (FIN) AF: 0.114 AC: 662 AN: 5788

Middle Eastern (MID) AF: 0.214 AC: 45 AN: 210

European-Non Finnish (NFE) AF: 0.159 AC: 8415 AN: 52762

Other (OTH) AF: 0.291 AC: 436 AN: 1497

Alfa AF: 0.0792 Hom.: 364

Bravo AF: 0.366

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.39
DANN	Benign	0.53
PhyloP100		-2.4

Splicing

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

Other links and lift over

dbSNP: rs6525177; hg19: chrX-66726506;