chrX-75780114-G-T

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

LOC107985664 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107985664	XR_001755892.2	n.822-11178G>T		intron_variant	Intron 3 of 3
LOC107985664	XR_001755894.2	n.822-11568G>T		intron_variant	Intron 3 of 3
LOC107985664	XR_007068272.1	n.958-11568G>T		intron_variant	Intron 4 of 4
LOC107985664	XR_007068273.1	n.822-11178G>T		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.182 AC: 20092 AN: 110613 Hom.: 1959 Cov.: 23 AF XY: 0.187 AC XY: 6144 AN XY: 32839

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

Gnomad4 AFR AF: 0.116

Gnomad4 AMR AF: 0.285

Gnomad4 ASJ AF: 0.119

Gnomad4 EAS AF: 0.854

Gnomad4 SAS AF: 0.364

Gnomad4 FIN AF: 0.169

Gnomad4 NFE AF: 0.153

Gnomad4 OTH AF: 0.177

Alfa AF: 0.173 Hom.: 9036

Bravo AF: 0.197

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1938012; hg19: chrX-74999949;