chrX-44648131-G-A

Position:

• chrX-44648131-G-A

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 0.163 in 110,875 control chromosomes in the GnomAD database, including 1,713 homozygotes. There are 5,584 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 0.16 (1713 hom., 5584 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.285

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.788 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: 0.163 AC: 18104 AN: 110822 Hom.: 1709 Cov.: 22 AF XY: 0.169 AC XY: 5574 AN XY: 33038

Gnomad AFR AF: 0.112

Gnomad AMI AF: 0.0355

Gnomad AMR AF: 0.278

Gnomad ASJ AF: 0.113

Gnomad EAS AF: 0.814

Gnomad SAS AF: 0.193

Gnomad FIN AF: 0.219

Gnomad MID AF: 0.0723

Gnomad NFE AF: 0.126

Gnomad OTH AF: 0.171

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

GnomAD4 genome AF: 0.163 AC: 18121 AN: 110875 Hom.: 1713 Cov.: 22 AF XY: 0.169 AC XY: 5584 AN XY: 33101

Gnomad4 AFR AF: 0.112

Gnomad4 AMR AF: 0.278

Gnomad4 ASJ AF: 0.113

Gnomad4 EAS AF: 0.813

Gnomad4 SAS AF: 0.194

Gnomad4 FIN AF: 0.219

Gnomad4 NFE AF: 0.126

Gnomad4 OTH AF: 0.180

Alfa AF: 0.160 Hom.: 2879

Bravo AF: 0.178

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.4
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5952606; hg19: chrX-44507377;