rs318125

Variant names:

• chrX-97948897-G-A
• rs318125

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.0126 in 111,916 control chromosomes in the GnomAD database, including 18 homozygotes. There are 485 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 0.013 (18 hom., 485 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.356
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BS1: Variant frequency is greater than expected in population amr. GnomAd4 allele frequency = 0.0126 (1413/111916) while in subpopulation AMR AF = 0.0456 (482/10563). AF 95% confidence interval is 0.0423. There are 18 homozygotes in GnomAd4. There are 485 alleles in the male GnomAd4 subpopulation. Median coverage is 23. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 18 gene

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: 0.0126 AC: 1408 AN: 111862 Hom.: 18 Cov.: 23

Gnomad AFR AF: 0.0244

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0457

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.0364

Gnomad SAS AF: 0.00374

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00424

Gnomad NFE AF: 0.000244

Gnomad OTH AF: 0.0159

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

GnomAD4 genome AF: 0.0126 AC: 1413 AN: 111916 Hom.: 18 Cov.: 23 AF XY: 0.0142 AC XY: 485 AN XY: 34120

African (AFR) AF: 0.0246 AC: 756 AN: 30790

American (AMR) AF: 0.0456 AC: 482 AN: 10563

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2648

East Asian (EAS) AF: 0.0359 AC: 127 AN: 3534

South Asian (SAS) AF: 0.00375 AC: 10 AN: 2666

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 6098

Middle Eastern (MID) AF: 0.00463 AC: 1 AN: 216

European-Non Finnish (NFE) AF: 0.000244 AC: 13 AN: 53187

Other (OTH) AF: 0.0157 AC: 24 AN: 1528

Alfa AF: 0.0135 Hom.: 52

Bravo AF: 0.0181

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	5.4
DANN	Benign	0.86
PhyloP100		0.36

Splicing

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

Other links and lift over

dbSNP: rs318125; hg19: chrX-97203895;