X-95824871-T-C

Variant names:

• chrX-95824871-T-C
• rs5990417

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 0.272 in 110,043 control chromosomes in the GnomAD database, including 4,813 homozygotes. There are 8,158 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 0.27 (4813 hom., 8158 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.568
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.594 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: 0.271 AC: 29863 AN: 110000 Hom.: 4807 Cov.: 23

Gnomad AFR AF: 0.602

Gnomad AMI AF: 0.118

Gnomad AMR AF: 0.160

Gnomad ASJ AF: 0.199

Gnomad EAS AF: 0.00447

Gnomad SAS AF: 0.0604

Gnomad FIN AF: 0.119

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.157

Gnomad OTH AF: 0.233

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

GnomAD4 genome AF: 0.272 AC: 29893 AN: 110043 Hom.: 4813 Cov.: 23 AF XY: 0.252 AC XY: 8158 AN XY: 32415

African (AFR) AF: 0.602 AC: 18122 AN: 30114

American (AMR) AF: 0.159 AC: 1634 AN: 10260

Ashkenazi Jewish (ASJ) AF: 0.199 AC: 523 AN: 2630

East Asian (EAS) AF: 0.00448 AC: 16 AN: 3569

South Asian (SAS) AF: 0.0603 AC: 161 AN: 2672

European-Finnish (FIN) AF: 0.119 AC: 688 AN: 5762

Middle Eastern (MID) AF: 0.251 AC: 54 AN: 215

European-Non Finnish (NFE) AF: 0.157 AC: 8271 AN: 52649

Other (OTH) AF: 0.230 AC: 344 AN: 1494

Alfa AF: 0.254 Hom.: 9335

Bravo AF: 0.290

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.9
DANN	Benign	0.67
PhyloP100		0.57

Splicing

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

Other links and lift over

dbSNP: rs5990417; hg19: chrX-95079870;