chrX-43747786-T-G

Variant names:

• chrX-43747786-T-G
• rs3027409

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;