rs5913038

Variant names:

• chrX-79710180-A-G
• rs5913038

Your query was ambiguous. Multiple possible variants found:

• chrX-79710180-A-G
• chrX-79710180-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 0.183 in 111,120 control chromosomes in the GnomAD database, including 1,597 homozygotes. There are 5,933 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 0.18 (1597 hom., 5933 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.383
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.342 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: 0.183 AC: 20297 AN: 111070 Hom.: 1594 Cov.: 23

Gnomad AFR AF: 0.0954

Gnomad AMI AF: 0.100

Gnomad AMR AF: 0.351

Gnomad ASJ AF: 0.188

Gnomad EAS AF: 0.240

Gnomad SAS AF: 0.113

Gnomad FIN AF: 0.192

Gnomad MID AF: 0.131

Gnomad NFE AF: 0.200

Gnomad OTH AF: 0.187

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

GnomAD4 genome AF: 0.183 AC: 20303 AN: 111120 Hom.: 1597 Cov.: 23 AF XY: 0.178 AC XY: 5933 AN XY: 33380

African (AFR) AF: 0.0953 AC: 2931 AN: 30760

American (AMR) AF: 0.351 AC: 3668 AN: 10437

Ashkenazi Jewish (ASJ) AF: 0.188 AC: 495 AN: 2639

East Asian (EAS) AF: 0.240 AC: 845 AN: 3525

South Asian (SAS) AF: 0.113 AC: 297 AN: 2636

European-Finnish (FIN) AF: 0.192 AC: 1136 AN: 5906

Middle Eastern (MID) AF: 0.140 AC: 30 AN: 215

European-Non Finnish (NFE) AF: 0.200 AC: 10546 AN: 52800

Other (OTH) AF: 0.188 AC: 287 AN: 1523

Alfa AF: 0.196 Hom.: 1379

Bravo AF: 0.198

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	4.6
DANN	Benign	0.96
PhyloP100		0.38

Splicing

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

Other links and lift over

dbSNP: rs5913038; hg19: chrX-78965677;