rs7060450

Variant names:

• chrX-116222536-A-C
• rs7060450

Your query was ambiguous. Multiple possible variants found:

• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;