rs7060450

Positions:

• chrX-116222536-A-C
• chrX-116222536-A-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 0.463 in 109,382 control chromosomes in the GnomAD database, including 9,157 homozygotes. There are 14,130 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 0.46 (9157 hom., 14130 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.967

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.618 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.463 AC: 50584 AN: 109338 Hom.: 9155 Cov.: 22 AF XY: 0.446 AC XY: 14107 AN XY: 31654

Gnomad AFR AF: 0.625

Gnomad AMI AF: 0.412

Gnomad AMR AF: 0.294

Gnomad ASJ AF: 0.365

Gnomad EAS AF: 0.223

Gnomad SAS AF: 0.422

Gnomad FIN AF: 0.428

Gnomad MID AF: 0.507

Gnomad NFE AF: 0.431

Gnomad OTH AF: 0.423

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

GnomAD4 genome AF: 0.463 AC: 50600 AN: 109382 Hom.: 9157 Cov.: 22 AF XY: 0.446 AC XY: 14130 AN XY: 31708

Gnomad4 AFR AF: 0.625

Gnomad4 AMR AF: 0.293

Gnomad4 ASJ AF: 0.365

Gnomad4 EAS AF: 0.224

Gnomad4 SAS AF: 0.422

Gnomad4 FIN AF: 0.428

Gnomad4 NFE AF: 0.431

Gnomad4 OTH AF: 0.421

Alfa AF: 0.438 Hom.: 4593

Bravo AF: 0.461

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.2
DANN	Benign	0.86

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7060450; hg19: chrX-115353791;