rs2056688

Variant names:

• chrX-4148702-G-A
• rs2056688

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 0.312 in 110,027 control chromosomes in the GnomAD database, including 4,152 homozygotes. There are 9,888 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 (4152 hom., 9888 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.790
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.574 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: 0.313 AC: 34369 AN: 109975 Hom.: 4154 Cov.: 22

Gnomad AFR AF: 0.340

Gnomad AMI AF: 0.138

Gnomad AMR AF: 0.444

Gnomad ASJ AF: 0.218

Gnomad EAS AF: 0.597

Gnomad SAS AF: 0.308

Gnomad FIN AF: 0.274

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.264

Gnomad OTH AF: 0.321

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

GnomAD4 genome AF: 0.312 AC: 34376 AN: 110027 Hom.: 4152 Cov.: 22 AF XY: 0.306 AC XY: 9888 AN XY: 32337

African (AFR) AF: 0.340 AC: 10271 AN: 30242

American (AMR) AF: 0.445 AC: 4545 AN: 10222

Ashkenazi Jewish (ASJ) AF: 0.218 AC: 574 AN: 2630

East Asian (EAS) AF: 0.596 AC: 2044 AN: 3432

South Asian (SAS) AF: 0.308 AC: 793 AN: 2577

European-Finnish (FIN) AF: 0.274 AC: 1585 AN: 5784

Middle Eastern (MID) AF: 0.296 AC: 63 AN: 213

European-Non Finnish (NFE) AF: 0.264 AC: 13935 AN: 52765

Other (OTH) AF: 0.318 AC: 473 AN: 1488

Alfa AF: 0.294 Hom.: 28342

Bravo AF: 0.335

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.11
DANN	Benign	0.53
PhyloP100		-0.79

Splicing

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

Other links and lift over

dbSNP: rs2056688; hg19: chrX-4066743;