chrX-71204561-G-A

Variant names:

• chrX-71204561-G-A
• rs6525480

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

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 0.29 (4103 hom., 8706 hem., cov: 20)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.185
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.715 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: 0.293 AC: 31415 AN: 107170 Hom.: 4098 Cov.: 20

Gnomad AFR AF: 0.397

Gnomad AMI AF: 0.139

Gnomad AMR AF: 0.405

Gnomad ASJ AF: 0.208

Gnomad EAS AF: 0.740

Gnomad SAS AF: 0.464

Gnomad FIN AF: 0.222

Gnomad MID AF: 0.145

Gnomad NFE AF: 0.192

Gnomad OTH AF: 0.292

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

GnomAD4 genome AF: 0.293 AC: 31442 AN: 107224 Hom.: 4103 Cov.: 20 AF XY: 0.292 AC XY: 8706 AN XY: 29782

African (AFR) AF: 0.397 AC: 11646 AN: 29342

American (AMR) AF: 0.405 AC: 3919 AN: 9673

Ashkenazi Jewish (ASJ) AF: 0.208 AC: 541 AN: 2598

East Asian (EAS) AF: 0.740 AC: 2459 AN: 3324

South Asian (SAS) AF: 0.462 AC: 1129 AN: 2446

European-Finnish (FIN) AF: 0.222 AC: 1199 AN: 5396

Middle Eastern (MID) AF: 0.141 AC: 30 AN: 213

European-Non Finnish (NFE) AF: 0.192 AC: 9993 AN: 52123

Other (OTH) AF: 0.300 AC: 433 AN: 1442

Alfa AF: 0.254 Hom.: 1579

Bravo AF: 0.318

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.0
DANN	Benign	0.66
PhyloP100		0.18

Splicing

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

Other links and lift over

dbSNP: rs6525480; hg19: chrX-70424411;