rs6611365

Positions:

• chrX-47314877-G-A
• chrX-47314877-G-T

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 0.214 in 110,414 control chromosomes in the GnomAD database, including 2,227 homozygotes. There are 7,419 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 0.21 (2227 hom., 7419 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.151

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 (SAS) allele frequency at 95% confidence interval = 0.514 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.214 AC: 23638 AN: 110360 Hom.: 2222 Cov.: 22 AF XY: 0.227 AC XY: 7408 AN XY: 32632

Gnomad AFR AF: 0.0808

Gnomad AMI AF: 0.366

Gnomad AMR AF: 0.388

Gnomad ASJ AF: 0.343

Gnomad EAS AF: 0.482

Gnomad SAS AF: 0.537

Gnomad FIN AF: 0.266

Gnomad MID AF: 0.262

Gnomad NFE AF: 0.210

Gnomad OTH AF: 0.231

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

GnomAD4 genome AF: 0.214 AC: 23655 AN: 110414 Hom.: 2227 Cov.: 22 AF XY: 0.227 AC XY: 7419 AN XY: 32696

Gnomad4 AFR AF: 0.0808

Gnomad4 AMR AF: 0.388

Gnomad4 ASJ AF: 0.343

Gnomad4 EAS AF: 0.482

Gnomad4 SAS AF: 0.537

Gnomad4 FIN AF: 0.266

Gnomad4 NFE AF: 0.210

Gnomad4 OTH AF: 0.241

Alfa AF: 0.234 Hom.: 21560

Bravo AF: 0.226

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.5
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6611365; hg19: chrX-47174276;