rs4969549

Positions:

• chrX-24247832-A-G
• chrX-24247832-A-T

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 0.414 in 109,998 control chromosomes in the GnomAD database, including 7,832 homozygotes. There are 13,248 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 0.41 (7832 hom., 13248 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.175

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.552 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.414 AC: 45490 AN: 109944 Hom.: 7833 Cov.: 23 AF XY: 0.409 AC XY: 13236 AN XY: 32370

Gnomad AFR AF: 0.174

Gnomad AMI AF: 0.647

Gnomad AMR AF: 0.564

Gnomad ASJ AF: 0.435

Gnomad EAS AF: 0.480

Gnomad SAS AF: 0.195

Gnomad FIN AF: 0.472

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.518

Gnomad OTH AF: 0.453

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

GnomAD4 genome AF: 0.414 AC: 45495 AN: 109998 Hom.: 7832 Cov.: 23 AF XY: 0.408 AC XY: 13248 AN XY: 32434

Gnomad4 AFR AF: 0.174

Gnomad4 AMR AF: 0.564

Gnomad4 ASJ AF: 0.435

Gnomad4 EAS AF: 0.479

Gnomad4 SAS AF: 0.196

Gnomad4 FIN AF: 0.472

Gnomad4 NFE AF: 0.518

Gnomad4 OTH AF: 0.451

Alfa AF: 0.350 Hom.: 2527

Bravo AF: 0.423

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	4.6
DANN	Benign	0.88

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4969549; hg19: chrX-24265949;