rs1349916

Positions:

• chrX-122626457-A-G

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 0.123 in 111,632 control chromosomes in the GnomAD database, including 682 homozygotes. There are 3,923 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 0.12 (682 hom., 3923 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00700

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.176 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: 0.123 AC: 13722 AN: 111577 Hom.: 683 Cov.: 23 AF XY: 0.116 AC XY: 3917 AN XY: 33811

Gnomad AFR AF: 0.180

Gnomad AMI AF: 0.199

Gnomad AMR AF: 0.0976

Gnomad ASJ AF: 0.136

Gnomad EAS AF: 0.137

Gnomad SAS AF: 0.136

Gnomad FIN AF: 0.0849

Gnomad MID AF: 0.0979

Gnomad NFE AF: 0.0969

Gnomad OTH AF: 0.110

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

GnomAD4 genome AF: 0.123 AC: 13729 AN: 111632 Hom.: 682 Cov.: 23 AF XY: 0.116 AC XY: 3923 AN XY: 33876

Gnomad4 AFR AF: 0.180

Gnomad4 AMR AF: 0.0977

Gnomad4 ASJ AF: 0.136

Gnomad4 EAS AF: 0.138

Gnomad4 SAS AF: 0.136

Gnomad4 FIN AF: 0.0849

Gnomad4 NFE AF: 0.0969

Gnomad4 OTH AF: 0.111

Alfa AF: 0.103 Hom.: 7166

Bravo AF: 0.128

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.89
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1349916; hg19: chrX-121760310;