chrX-43029755-T-C

Variant names:

• chrX-43029755-T-C
• rs5991545

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 0.171 in 111,035 control chromosomes in the GnomAD database, including 3,277 homozygotes. There are 5,310 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 0.17 (3277 hom., 5310 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.968

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.519 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: 0.171 AC: 18928 AN: 110998 Hom.: 3275 Cov.: 23 AF XY: 0.159 AC XY: 5291 AN XY: 33304

Gnomad AFR AF: 0.526

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0830

Gnomad ASJ AF: 0.00754

Gnomad EAS AF: 0.245

Gnomad SAS AF: 0.141

Gnomad FIN AF: 0.0282

Gnomad MID AF: 0.0302

Gnomad NFE AF: 0.00826

Gnomad OTH AF: 0.141

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

GnomAD4 genome AF: 0.171 AC: 18959 AN: 111035 Hom.: 3277 Cov.: 23 AF XY: 0.159 AC XY: 5310 AN XY: 33351

Gnomad4 AFR AF: 0.526

Gnomad4 AMR AF: 0.0827

Gnomad4 ASJ AF: 0.00754

Gnomad4 EAS AF: 0.245

Gnomad4 SAS AF: 0.142

Gnomad4 FIN AF: 0.0282

Gnomad4 NFE AF: 0.00826

Gnomad4 OTH AF: 0.143

Alfa AF: 0.0994 Hom.: 625

Bravo AF: 0.196

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.5
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5991545; hg19: chrX-42889004;