X-143075435-C-T

Variant names:

• chrX-143075435-C-T
• rs1997686

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 0.311 in 110,307 control chromosomes in the GnomAD database, including 4,470 homozygotes. There are 9,708 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 0.31 (4470 hom., 9708 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.504
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.495 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.311 AC: 34282 AN: 110258 Hom.: 4465 Cov.: 22

Gnomad AFR AF: 0.501

Gnomad AMI AF: 0.244

Gnomad AMR AF: 0.366

Gnomad ASJ AF: 0.280

Gnomad EAS AF: 0.349

Gnomad SAS AF: 0.196

Gnomad FIN AF: 0.193

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.209

Gnomad OTH AF: 0.349

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

GnomAD4 genome AF: 0.311 AC: 34325 AN: 110307 Hom.: 4470 Cov.: 22 AF XY: 0.298 AC XY: 9708 AN XY: 32591

African (AFR) AF: 0.501 AC: 15143 AN: 30201

American (AMR) AF: 0.367 AC: 3778 AN: 10303

Ashkenazi Jewish (ASJ) AF: 0.280 AC: 736 AN: 2632

East Asian (EAS) AF: 0.348 AC: 1207 AN: 3469

South Asian (SAS) AF: 0.196 AC: 513 AN: 2615

European-Finnish (FIN) AF: 0.193 AC: 1127 AN: 5853

Middle Eastern (MID) AF: 0.325 AC: 69 AN: 212

European-Non Finnish (NFE) AF: 0.209 AC: 11066 AN: 52844

Other (OTH) AF: 0.346 AC: 522 AN: 1507

Alfa AF: 0.249 Hom.: 27389

Bravo AF: 0.342

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.1
DANN	Benign	0.40
PhyloP100		0.50

Splicing

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

Other links and lift over

dbSNP: rs1997686; hg19: chrX-142163221;