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. The variant received -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
• Publications: 1 publications found

ACMG classification

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

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

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.463 AC: 50584 AN: 109338 Hom.: 9155 Cov.: 22

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

African (AFR) AF: 0.625 AC: 18750 AN: 29991

American (AMR) AF: 0.293 AC: 3011 AN: 10282

Ashkenazi Jewish (ASJ) AF: 0.365 AC: 960 AN: 2627

East Asian (EAS) AF: 0.224 AC: 768 AN: 3436

South Asian (SAS) AF: 0.422 AC: 1076 AN: 2551

European-Finnish (FIN) AF: 0.428 AC: 2382 AN: 5564

Middle Eastern (MID) AF: 0.502 AC: 104 AN: 207

European-Non Finnish (NFE) AF: 0.431 AC: 22635 AN: 52540

Other (OTH) AF: 0.421 AC: 636 AN: 1510

Alfa AF: 0.438 Hom.: 4593

Bravo AF: 0.461

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.2
DANN	Benign	0.86
PhyloP100		-0.97

Splicing

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

Other links and lift over

dbSNP: rs7060450; hg19: chrX-115353791;