rs3975394

Variant names:

• chrX-143167934-C-T
• rs3975394

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 0.247 in 110,491 control chromosomes in the GnomAD database, including 2,567 homozygotes. There are 7,897 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 0.25 (2567 hom., 7897 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.321
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.264 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: 0.247 AC: 27305 AN: 110437 Hom.: 2566 Cov.: 22

Gnomad AFR AF: 0.249

Gnomad AMI AF: 0.218

Gnomad AMR AF: 0.170

Gnomad ASJ AF: 0.278

Gnomad EAS AF: 0.0485

Gnomad SAS AF: 0.128

Gnomad FIN AF: 0.352

Gnomad MID AF: 0.318

Gnomad NFE AF: 0.268

Gnomad OTH AF: 0.241

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

GnomAD4 genome AF: 0.247 AC: 27317 AN: 110491 Hom.: 2567 Cov.: 22 AF XY: 0.241 AC XY: 7897 AN XY: 32743

African (AFR) AF: 0.249 AC: 7569 AN: 30384

American (AMR) AF: 0.169 AC: 1771 AN: 10458

Ashkenazi Jewish (ASJ) AF: 0.278 AC: 729 AN: 2623

East Asian (EAS) AF: 0.0476 AC: 165 AN: 3470

South Asian (SAS) AF: 0.129 AC: 330 AN: 2566

European-Finnish (FIN) AF: 0.352 AC: 2051 AN: 5828

Middle Eastern (MID) AF: 0.321 AC: 68 AN: 212

European-Non Finnish (NFE) AF: 0.268 AC: 14116 AN: 52750

Other (OTH) AF: 0.243 AC: 371 AN: 1525

Alfa AF: 0.258 Hom.: 28002

Bravo AF: 0.234

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.9
DANN	Benign	0.43
PhyloP100		0.32

Splicing

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

Other links and lift over

dbSNP: rs3975394; hg19: chrX-142255720;