rs4132871

Variant names:

• chrX-135468448-C-T
• rs4132871

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 0.395 in 110,851 control chromosomes in the GnomAD database, including 6,300 homozygotes. There are 12,843 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 0.39 (6300 hom., 12843 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.593
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.544 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: 0.395 AC: 43732 AN: 110802 Hom.: 6302 Cov.: 22

Gnomad AFR AF: 0.347

Gnomad AMI AF: 0.375

Gnomad AMR AF: 0.299

Gnomad ASJ AF: 0.457

Gnomad EAS AF: 0.520

Gnomad SAS AF: 0.567

Gnomad FIN AF: 0.390

Gnomad MID AF: 0.566

Gnomad NFE AF: 0.420

Gnomad OTH AF: 0.415

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

GnomAD4 genome AF: 0.395 AC: 43756 AN: 110851 Hom.: 6300 Cov.: 22 AF XY: 0.388 AC XY: 12843 AN XY: 33137

African (AFR) AF: 0.347 AC: 10605 AN: 30526

American (AMR) AF: 0.300 AC: 3137 AN: 10462

Ashkenazi Jewish (ASJ) AF: 0.457 AC: 1206 AN: 2639

East Asian (EAS) AF: 0.520 AC: 1814 AN: 3490

South Asian (SAS) AF: 0.567 AC: 1512 AN: 2665

European-Finnish (FIN) AF: 0.390 AC: 2291 AN: 5881

Middle Eastern (MID) AF: 0.565 AC: 121 AN: 214

European-Non Finnish (NFE) AF: 0.420 AC: 22197 AN: 52791

Other (OTH) AF: 0.411 AC: 623 AN: 1516

Alfa AF: 0.400 Hom.: 21439

Bravo AF: 0.383

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.73
PhyloP100		-0.59

Splicing

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

Other links and lift over

dbSNP: rs4132871; hg19: chrX-134602373;