rs1074568

Variant names:

• chrX-138313358-G-A
• rs1074568

Your query was ambiguous. Multiple possible variants found:

• chrX-138313358-G-A
• chrX-138313358-G-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 0.0722 in 110,356 control chromosomes in the GnomAD database, including 613 homozygotes. There are 2,085 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 0.072 (613 hom., 2085 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.831
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.228 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: 0.0721 AC: 7948 AN: 110303 Hom.: 612 Cov.: 22

Gnomad AFR AF: 0.232

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0293

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00344

Gnomad FIN AF: 0.00619

Gnomad MID AF: 0.00851

Gnomad NFE AF: 0.00956

Gnomad OTH AF: 0.0590

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

GnomAD4 genome AF: 0.0722 AC: 7968 AN: 110356 Hom.: 613 Cov.: 22 AF XY: 0.0636 AC XY: 2085 AN XY: 32784

African (AFR) AF: 0.232 AC: 7026 AN: 30228

American (AMR) AF: 0.0293 AC: 303 AN: 10344

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2625

East Asian (EAS) AF: 0.00 AC: 0 AN: 3497

South Asian (SAS) AF: 0.00345 AC: 9 AN: 2607

European-Finnish (FIN) AF: 0.00619 AC: 37 AN: 5977

Middle Eastern (MID) AF: 0.00930 AC: 2 AN: 215

European-Non Finnish (NFE) AF: 0.00957 AC: 504 AN: 52688

Other (OTH) AF: 0.0583 AC: 87 AN: 1493

Alfa AF: 0.0121 Hom.: 66

Bravo AF: 0.0810

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.26
DANN	Benign	0.41
PhyloP100		-0.83

Splicing

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

Other links and lift over

dbSNP: rs1074568; hg19: chrX-137395517;