rs6654819

Variant names:

• chrX-6540125-G-A
• rs6654819

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 0.17 in 110,634 control chromosomes in the GnomAD database, including 2,507 homozygotes. There are 5,159 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 0.17 (2507 hom., 5159 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.320
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.453 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.170 AC: 18783 AN: 110585 Hom.: 2506 Cov.: 22

Gnomad AFR AF: 0.459

Gnomad AMI AF: 0.0621

Gnomad AMR AF: 0.0960

Gnomad ASJ AF: 0.0711

Gnomad EAS AF: 0.00113

Gnomad SAS AF: 0.0870

Gnomad FIN AF: 0.0251

Gnomad MID AF: 0.0936

Gnomad NFE AF: 0.0583

Gnomad OTH AF: 0.144

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

GnomAD4 genome AF: 0.170 AC: 18821 AN: 110634 Hom.: 2507 Cov.: 22 AF XY: 0.157 AC XY: 5159 AN XY: 32920

African (AFR) AF: 0.459 AC: 13895 AN: 30253

American (AMR) AF: 0.0960 AC: 998 AN: 10400

Ashkenazi Jewish (ASJ) AF: 0.0711 AC: 188 AN: 2643

East Asian (EAS) AF: 0.00114 AC: 4 AN: 3514

South Asian (SAS) AF: 0.0865 AC: 226 AN: 2613

European-Finnish (FIN) AF: 0.0251 AC: 148 AN: 5898

Middle Eastern (MID) AF: 0.0981 AC: 21 AN: 214

European-Non Finnish (NFE) AF: 0.0583 AC: 3085 AN: 52918

Other (OTH) AF: 0.142 AC: 214 AN: 1505

Alfa AF: 0.102 Hom.: 7676

Bravo AF: 0.189

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.3
DANN	Benign	0.64
PhyloP100		0.32

Splicing

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

Other links and lift over

dbSNP: rs6654819; hg19: chrX-6458166;