X-51573615-A-G

Variant names:

• chrX-51573615-A-G
• rs3131301

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 0.0229 in 111,997 control chromosomes in the GnomAD database, including 33 homozygotes. There are 770 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 0.023 (33 hom., 770 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.83
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0229 (2563/111997) while in subpopulation NFE AF = 0.0358 (1903/53208). AF 95% confidence interval is 0.0344. There are 33 homozygotes in GnomAd4. There are 770 alleles in the male GnomAd4 subpopulation. Median coverage is 23. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 33 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: 0.0229 AC: 2564 AN: 111952 Hom.: 33 Cov.: 23

Gnomad AFR AF: 0.00480

Gnomad AMI AF: 0.0543

Gnomad AMR AF: 0.0201

Gnomad ASJ AF: 0.00945

Gnomad EAS AF: 0.000278

Gnomad SAS AF: 0.0182

Gnomad FIN AF: 0.0218

Gnomad MID AF: 0.0636

Gnomad NFE AF: 0.0358

Gnomad OTH AF: 0.0285

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

GnomAD4 genome AF: 0.0229 AC: 2563 AN: 111997 Hom.: 33 Cov.: 23 AF XY: 0.0225 AC XY: 770 AN XY: 34161

African (AFR) AF: 0.00479 AC: 148 AN: 30884

American (AMR) AF: 0.0201 AC: 211 AN: 10506

Ashkenazi Jewish (ASJ) AF: 0.00945 AC: 25 AN: 2646

East Asian (EAS) AF: 0.000279 AC: 1 AN: 3587

South Asian (SAS) AF: 0.0179 AC: 48 AN: 2686

European-Finnish (FIN) AF: 0.0218 AC: 132 AN: 6060

Middle Eastern (MID) AF: 0.0701 AC: 15 AN: 214

European-Non Finnish (NFE) AF: 0.0358 AC: 1903 AN: 53208

Other (OTH) AF: 0.0282 AC: 43 AN: 1525

Alfa AF: 0.0343 Hom.: 1289

Bravo AF: 0.0224

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.9
DANN	Benign	0.85
PhyloP100		1.8

Splicing

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

Other links and lift over

dbSNP: rs3131301; hg19: chrX-51316467;