chrX-43029755-T-C

Variant names:

• chrX-43029755-T-C
• rs5991545

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.171 AC: 18928 AN: 110998 Hom.: 3275 Cov.: 23

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

African (AFR) AF: 0.526 AC: 16005 AN: 30428

American (AMR) AF: 0.0827 AC: 864 AN: 10446

Ashkenazi Jewish (ASJ) AF: 0.00754 AC: 20 AN: 2652

East Asian (EAS) AF: 0.245 AC: 859 AN: 3499

South Asian (SAS) AF: 0.142 AC: 383 AN: 2701

European-Finnish (FIN) AF: 0.0282 AC: 166 AN: 5878

Middle Eastern (MID) AF: 0.0333 AC: 7 AN: 210

European-Non Finnish (NFE) AF: 0.00826 AC: 438 AN: 53023

Other (OTH) AF: 0.143 AC: 217 AN: 1513

Alfa AF: 0.0994 Hom.: 625

Bravo AF: 0.196

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.5
DANN	Benign	0.61
PhyloP100		0.97

Splicing

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

Other links and lift over

dbSNP: rs5991545; hg19: chrX-42889004;