chrX-6300992-C-T

Variant names:

• chrX-6300992-C-T
• rs1840485

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 0.304 in 111,150 control chromosomes in the GnomAD database, including 4,220 homozygotes. There are 9,625 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 0.30 (4220 hom., 9625 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.720
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.458 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: 0.304 AC: 33763 AN: 111096 Hom.: 4219 Cov.: 23

Gnomad AFR AF: 0.463

Gnomad AMI AF: 0.284

Gnomad AMR AF: 0.263

Gnomad ASJ AF: 0.253

Gnomad EAS AF: 0.0830

Gnomad SAS AF: 0.176

Gnomad FIN AF: 0.212

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.256

Gnomad OTH AF: 0.290

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

GnomAD4 genome AF: 0.304 AC: 33804 AN: 111150 Hom.: 4220 Cov.: 23 AF XY: 0.288 AC XY: 9625 AN XY: 33400

African (AFR) AF: 0.464 AC: 14135 AN: 30461

American (AMR) AF: 0.263 AC: 2758 AN: 10497

Ashkenazi Jewish (ASJ) AF: 0.253 AC: 667 AN: 2637

East Asian (EAS) AF: 0.0827 AC: 291 AN: 3519

South Asian (SAS) AF: 0.176 AC: 470 AN: 2672

European-Finnish (FIN) AF: 0.212 AC: 1263 AN: 5966

Middle Eastern (MID) AF: 0.209 AC: 45 AN: 215

European-Non Finnish (NFE) AF: 0.256 AC: 13554 AN: 53004

Other (OTH) AF: 0.286 AC: 432 AN: 1513

Alfa AF: 0.251 Hom.: 7450

Bravo AF: 0.318

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.41
DANN	Benign	0.47
PhyloP100		-0.72

Splicing

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

Other links and lift over

dbSNP: rs1840485; hg19: chrX-6219033;