rs1600719

Variant names:

• chrX-122278223-A-T
• rs1600719

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.221 AC: 24489 AN: 110935 Hom.: 2051 Cov.: 23 AF XY: 0.211 AC XY: 7002 AN XY: 33243

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

Gnomad4 AFR AF: 0.155

Gnomad4 AMR AF: 0.194

Gnomad4 ASJ AF: 0.323

Gnomad4 EAS AF: 0.139

Gnomad4 SAS AF: 0.134

Gnomad4 FIN AF: 0.235

Gnomad4 NFE AF: 0.268

Gnomad4 OTH AF: 0.233

Alfa AF: 0.238 Hom.: 1464

Bravo AF: 0.215

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1600719; hg19: chrX-121412076;