X-75780114-G-T

Variant names:

• chrX-75780114-G-T
• rs1938012
• XR_001755892.2:n.822-11178G>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_001755892.2(LOC107985664):​n.822-11178G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.182 in 110,666 control chromosomes in the GnomAD database, including 1,963 homozygotes. There are 6,150 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 (1963 hom., 6150 hem., cov: 23)
• Consequence: LOC107985664 XR_001755892.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.554
• Publications: 1 publications found

Genes affected

LOC107985664 (HGNC:):

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 = 0.828 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.182 AC: 20092 AN: 110613 Hom.: 1959 Cov.: 23

Gnomad AFR AF: 0.116

Gnomad AMI AF: 0.0957

Gnomad AMR AF: 0.285

Gnomad ASJ AF: 0.119

Gnomad EAS AF: 0.853

Gnomad SAS AF: 0.364

Gnomad FIN AF: 0.169

Gnomad MID AF: 0.119

Gnomad NFE AF: 0.153

Gnomad OTH AF: 0.170

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

GnomAD4 genome AF: 0.182 AC: 20106 AN: 110666 Hom.: 1963 Cov.: 23 AF XY: 0.187 AC XY: 6150 AN XY: 32902

African (AFR) AF: 0.116 AC: 3522 AN: 30461

American (AMR) AF: 0.285 AC: 2964 AN: 10407

Ashkenazi Jewish (ASJ) AF: 0.119 AC: 312 AN: 2632

East Asian (EAS) AF: 0.854 AC: 2944 AN: 3449

South Asian (SAS) AF: 0.364 AC: 942 AN: 2591

European-Finnish (FIN) AF: 0.169 AC: 991 AN: 5870

Middle Eastern (MID) AF: 0.121 AC: 26 AN: 215

European-Non Finnish (NFE) AF: 0.153 AC: 8073 AN: 52857

Other (OTH) AF: 0.177 AC: 267 AN: 1505

Alfa AF: 0.174 Hom.: 12929

Bravo AF: 0.197

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.8
DANN	Benign	0.67
PhyloP100		0.55

Splicing

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

Other links and lift over

dbSNP: rs1938012; hg19: chrX-74999949;