rs4969549

Variant names:

• chrX-24247832-A-G
• rs4969549

Your query was ambiguous. Multiple possible variants found:

• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;