chrX-147961254-C-T

Variant names:

• chrX-147961254-C-T
• rs5904818

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 0.133 in 111,310 control chromosomes in the GnomAD database, including 1,314 homozygotes. There are 4,091 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 0.13 (1314 hom., 4091 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.331
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.319 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: 0.133 AC: 14820 AN: 111258 Hom.: 1316 Cov.: 23

Gnomad AFR AF: 0.325

Gnomad AMI AF: 0.0176

Gnomad AMR AF: 0.0602

Gnomad ASJ AF: 0.0423

Gnomad EAS AF: 0.00198

Gnomad SAS AF: 0.115

Gnomad FIN AF: 0.0248

Gnomad MID AF: 0.119

Gnomad NFE AF: 0.0664

Gnomad OTH AF: 0.124

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

GnomAD4 genome AF: 0.133 AC: 14826 AN: 111310 Hom.: 1314 Cov.: 23 AF XY: 0.122 AC XY: 4091 AN XY: 33558

African (AFR) AF: 0.325 AC: 9869 AN: 30410

American (AMR) AF: 0.0601 AC: 636 AN: 10575

Ashkenazi Jewish (ASJ) AF: 0.0423 AC: 112 AN: 2648

East Asian (EAS) AF: 0.00198 AC: 7 AN: 3531

South Asian (SAS) AF: 0.114 AC: 304 AN: 2656

European-Finnish (FIN) AF: 0.0248 AC: 150 AN: 6052

Middle Eastern (MID) AF: 0.121 AC: 26 AN: 215

European-Non Finnish (NFE) AF: 0.0664 AC: 3522 AN: 53024

Other (OTH) AF: 0.124 AC: 188 AN: 1517

Alfa AF: 0.111 Hom.: 6573

Bravo AF: 0.146

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.65
DANN	Benign	0.81
PhyloP100		-0.33

Splicing

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

Other links and lift over

dbSNP: rs5904818; hg19: chrX-147042774;