rs4828879

Variant names:

• chrX-23643757-A-G
• rs4828879

Your query was ambiguous. Multiple possible variants found:

• chrX-23643757-A-G
• chrX-23643757-A-T

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 0.164 in 110,887 control chromosomes in the GnomAD database, including 1,644 homozygotes. There are 5,099 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 0.16 (1644 hom., 5099 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.167
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.329 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: 0.163 AC: 18090 AN: 110832 Hom.: 1642 Cov.: 22

Gnomad AFR AF: 0.317

Gnomad AMI AF: 0.0350

Gnomad AMR AF: 0.217

Gnomad ASJ AF: 0.0553

Gnomad EAS AF: 0.346

Gnomad SAS AF: 0.144

Gnomad FIN AF: 0.0481

Gnomad MID AF: 0.106

Gnomad NFE AF: 0.0738

Gnomad OTH AF: 0.165

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

GnomAD4 genome AF: 0.164 AC: 18131 AN: 110887 Hom.: 1644 Cov.: 22 AF XY: 0.154 AC XY: 5099 AN XY: 33159

African (AFR) AF: 0.318 AC: 9631 AN: 30333

American (AMR) AF: 0.218 AC: 2262 AN: 10362

Ashkenazi Jewish (ASJ) AF: 0.0553 AC: 146 AN: 2641

East Asian (EAS) AF: 0.345 AC: 1202 AN: 3485

South Asian (SAS) AF: 0.146 AC: 382 AN: 2619

European-Finnish (FIN) AF: 0.0481 AC: 289 AN: 6006

Middle Eastern (MID) AF: 0.108 AC: 23 AN: 213

European-Non Finnish (NFE) AF: 0.0739 AC: 3917 AN: 53030

Other (OTH) AF: 0.169 AC: 255 AN: 1512

Alfa AF: 0.123 Hom.: 9023

Bravo AF: 0.193

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.66
DANN	Benign	0.67
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs4828879; hg19: chrX-23661874;