chrX-122278223-A-T

Variant names:

• chrX-122278223-A-T
• rs1600719

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 0.221 in 110,986 control chromosomes in the GnomAD database, including 2,054 homozygotes. There are 7,009 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 0.22 (2054 hom., 7009 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.12
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.264 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: 0.221 AC: 24489 AN: 110935 Hom.: 2051 Cov.: 23

Gnomad AFR AF: 0.156

Gnomad AMI AF: 0.141

Gnomad AMR AF: 0.194

Gnomad ASJ AF: 0.323

Gnomad EAS AF: 0.139

Gnomad SAS AF: 0.133

Gnomad FIN AF: 0.235

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.268

Gnomad OTH AF: 0.225

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

GnomAD4 genome AF: 0.221 AC: 24502 AN: 110986 Hom.: 2054 Cov.: 23 AF XY: 0.210 AC XY: 7009 AN XY: 33304

African (AFR) AF: 0.155 AC: 4775 AN: 30756

American (AMR) AF: 0.194 AC: 2030 AN: 10473

Ashkenazi Jewish (ASJ) AF: 0.323 AC: 851 AN: 2634

East Asian (EAS) AF: 0.139 AC: 491 AN: 3527

South Asian (SAS) AF: 0.134 AC: 365 AN: 2717

European-Finnish (FIN) AF: 0.235 AC: 1378 AN: 5862

Middle Eastern (MID) AF: 0.311 AC: 64 AN: 206

European-Non Finnish (NFE) AF: 0.268 AC: 14099 AN: 52619

Other (OTH) AF: 0.233 AC: 353 AN: 1512

Alfa AF: 0.238 Hom.: 1464

Bravo AF: 0.215

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	5.7
DANN	Benign	0.60
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs1600719; hg19: chrX-121412076;