chrX-47314877-G-A

Variant names:

• chrX-47314877-G-A
• rs6611365

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -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

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

African (AFR) AF: 0.0808 AC: 2471 AN: 30597

American (AMR) AF: 0.388 AC: 3975 AN: 10245

Ashkenazi Jewish (ASJ) AF: 0.343 AC: 903 AN: 2634

East Asian (EAS) AF: 0.482 AC: 1646 AN: 3414

South Asian (SAS) AF: 0.537 AC: 1380 AN: 2568

European-Finnish (FIN) AF: 0.266 AC: 1540 AN: 5800

Middle Eastern (MID) AF: 0.264 AC: 57 AN: 216

European-Non Finnish (NFE) AF: 0.210 AC: 11077 AN: 52772

Other (OTH) AF: 0.241 AC: 362 AN: 1502

Alfa AF: 0.227 Hom.: 27087

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
PhyloP100		0.15

Splicing

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

Other links and lift over

dbSNP: rs6611365; hg19: chrX-47174276;