chrX-142842056-G-T

Variant names:

• chrX-142842056-G-T
• rs10521831

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 0.0982 in 111,902 control chromosomes in the GnomAD database, including 989 homozygotes. There are 3,223 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 0.098 (989 hom., 3223 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.557
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.283 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: 0.0980 AC: 10960 AN: 111850 Hom.: 986 Cov.: 23

Gnomad AFR AF: 0.288

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.101

Gnomad ASJ AF: 0.0287

Gnomad EAS AF: 0.104

Gnomad SAS AF: 0.0489

Gnomad FIN AF: 0.000490

Gnomad MID AF: 0.0730

Gnomad NFE AF: 0.00648

Gnomad OTH AF: 0.0879

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

GnomAD4 genome AF: 0.0982 AC: 10994 AN: 111902 Hom.: 989 Cov.: 23 AF XY: 0.0945 AC XY: 3223 AN XY: 34114

African (AFR) AF: 0.288 AC: 8852 AN: 30725

American (AMR) AF: 0.101 AC: 1066 AN: 10540

Ashkenazi Jewish (ASJ) AF: 0.0287 AC: 76 AN: 2646

East Asian (EAS) AF: 0.104 AC: 368 AN: 3550

South Asian (SAS) AF: 0.0491 AC: 132 AN: 2690

European-Finnish (FIN) AF: 0.000490 AC: 3 AN: 6122

Middle Eastern (MID) AF: 0.0704 AC: 15 AN: 213

European-Non Finnish (NFE) AF: 0.00650 AC: 346 AN: 53209

Other (OTH) AF: 0.0895 AC: 136 AN: 1520

Alfa AF: 0.0243 Hom.: 828

Bravo AF: 0.117

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.9
DANN	Benign	0.65
PhyloP100		0.56

Splicing

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

Other links and lift over

dbSNP: rs10521831; hg19: chrX-141929842;