rs6611365

Variant names:

• chrX-47314877-G-A
• rs6611365

Your query was ambiguous. Multiple possible variants found:

• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;