rs7049502

Positions:

• chrX-885443-G-C

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 0.0857 in 152,044 control chromosomes in the GnomAD database, including 689 homozygotes. There are 6,211 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 0.086 (689 hom., 6211 hem., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.336

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.142 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: 0.0856 AC: 13000 AN: 151926 Hom.: 679 Cov.: 32 AF XY: 0.0834 AC XY: 6187 AN XY: 74200

Gnomad AFR AF: 0.144

Gnomad AMI AF: 0.0482

Gnomad AMR AF: 0.0623

Gnomad ASJ AF: 0.0551

Gnomad EAS AF: 0.00598

Gnomad SAS AF: 0.126

Gnomad FIN AF: 0.0475

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0662

Gnomad OTH AF: 0.0902

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

GnomAD4 genome AF: 0.0857 AC: 13036 AN: 152044 Hom.: 689 Cov.: 32 AF XY: 0.0836 AC XY: 6211 AN XY: 74328

Gnomad4 AFR AF: 0.145

Gnomad4 AMR AF: 0.0624

Gnomad4 ASJ AF: 0.0551

Gnomad4 EAS AF: 0.00599

Gnomad4 SAS AF: 0.125

Gnomad4 FIN AF: 0.0475

Gnomad4 NFE AF: 0.0663

Gnomad4 OTH AF: 0.0907

Bravo AF: 0.0866

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	0.063
DANN	Benign	0.12

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7049502; hg19: chrX-846178;