X-47811022-G-T

Variant names:

• chrX-47811022-G-T
• rs1207463

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 0.0518 in 106,502 control chromosomes in the GnomAD database, including 317 homozygotes. There are 1,426 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 0.052 (317 hom., 1426 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.224
• Publications: 1 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 (AFR) allele frequency at 95% confidence interval = 0.175 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: 0.0518 AC: 5511 AN: 106466 Hom.: 318 Cov.: 22

Gnomad AFR AF: 0.179

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0218

Gnomad ASJ AF: 0.00116

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00881

Gnomad NFE AF: 0.000792

Gnomad OTH AF: 0.0486

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

GnomAD4 genome AF: 0.0518 AC: 5521 AN: 106502 Hom.: 317 Cov.: 22 AF XY: 0.0473 AC XY: 1426 AN XY: 30120

African (AFR) AF: 0.179 AC: 5191 AN: 29002

American (AMR) AF: 0.0216 AC: 214 AN: 9901

Ashkenazi Jewish (ASJ) AF: 0.00116 AC: 3 AN: 2585

East Asian (EAS) AF: 0.00 AC: 0 AN: 3396

South Asian (SAS) AF: 0.000410 AC: 1 AN: 2441

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 5081

Middle Eastern (MID) AF: 0.00971 AC: 2 AN: 206

European-Non Finnish (NFE) AF: 0.000792 AC: 41 AN: 51781

Other (OTH) AF: 0.0479 AC: 69 AN: 1441

Alfa AF: 0.0238 Hom.: 1361

Bravo AF: 0.0591

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	5.0
DANN	Benign	0.30
PhyloP100		0.22

Splicing

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

Other links and lift over

dbSNP: rs1207463; hg19: chrX-47670421;