X-83616187-A-G

Variant names:

• chrX-83616187-A-G
• rs5922838

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 0.2 in 110,365 control chromosomes in the GnomAD database, including 1,657 homozygotes. There are 6,436 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 0.20 (1657 hom., 6436 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0720
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.27 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: 0.200 AC: 22064 AN: 110314 Hom.: 1648 Cov.: 23

Gnomad AFR AF: 0.273

Gnomad AMI AF: 0.215

Gnomad AMR AF: 0.172

Gnomad ASJ AF: 0.185

Gnomad EAS AF: 0.278

Gnomad SAS AF: 0.285

Gnomad FIN AF: 0.191

Gnomad MID AF: 0.246

Gnomad NFE AF: 0.155

Gnomad OTH AF: 0.191

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

GnomAD4 genome AF: 0.200 AC: 22096 AN: 110365 Hom.: 1657 Cov.: 23 AF XY: 0.196 AC XY: 6436 AN XY: 32861

African (AFR) AF: 0.272 AC: 8319 AN: 30560

American (AMR) AF: 0.173 AC: 1788 AN: 10320

Ashkenazi Jewish (ASJ) AF: 0.185 AC: 484 AN: 2616

East Asian (EAS) AF: 0.277 AC: 969 AN: 3495

South Asian (SAS) AF: 0.287 AC: 767 AN: 2677

European-Finnish (FIN) AF: 0.191 AC: 1117 AN: 5853

Middle Eastern (MID) AF: 0.259 AC: 56 AN: 216

European-Non Finnish (NFE) AF: 0.155 AC: 8146 AN: 52441

Other (OTH) AF: 0.201 AC: 304 AN: 1509

Alfa AF: 0.172 Hom.: 6969

Bravo AF: 0.206

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	3.5
DANN	Benign	0.56
PhyloP100		0.072

Splicing

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

Other links and lift over

dbSNP: rs5922838; hg19: chrX-82871195;