rs3027409

chrX-43747786-T-G

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 0.0971 in 111,167 control chromosomes in the GnomAD database, including 761 homozygotes. There are 2,825 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 0.097 (761 hom., 2825 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.890

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.246 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0969 AC: 10772 AN: 111112 Hom.: 760 Cov.: 22 AF XY: 0.0841 AC XY: 2802 AN XY: 33336

Gnomad AFR AF: 0.250

Gnomad AMI AF: 0.0102

Gnomad AMR AF: 0.0537

Gnomad ASJ AF: 0.0726

Gnomad EAS AF: 0.000282

Gnomad SAS AF: 0.0206

Gnomad FIN AF: 0.0135

Gnomad MID AF: 0.0879

Gnomad NFE AF: 0.0404

Gnomad OTH AF: 0.0826

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

GnomAD4 genome AF: 0.0971 AC: 10799 AN: 111167 Hom.: 761 Cov.: 22 AF XY: 0.0846 AC XY: 2825 AN XY: 33401

Gnomad4 AFR AF: 0.251

Gnomad4 AMR AF: 0.0535

Gnomad4 ASJ AF: 0.0726

Gnomad4 EAS AF: 0.000283

Gnomad4 SAS AF: 0.0206

Gnomad4 FIN AF: 0.0135

Gnomad4 NFE AF: 0.0404

Gnomad4 OTH AF: 0.0815

Alfa AF: 0.0505 Hom.: 3849

Bravo AF: 0.109

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	5.2
Dann	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3027409; hg19: chrX-43607033;