X-42917700-T-C

Variant names:

• chrX-42917700-T-C
• rs205828
• ENST00000776509.1:n.125+29230A>G

Variant summary

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

The ENST00000776509.1(ENSG00000301130):​n.125+29230A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.331 in 110,912 control chromosomes in the GnomAD database, including 5,802 homozygotes. There are 10,464 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 0.33 (5802 hom., 10464 hem., cov: 22)
• Consequence: ENSG00000301130 ENST00000776509.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.413
• Publications: 0 publications found

Genes affected

ENSG00000301130 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.613 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
ENSG00000301130	ENST00000776509.1	n.125+29230A>G		intron_variant	Intron 1 of 3
ENSG00000301130	ENST00000776510.1	n.89-2335A>G		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.331 AC: 36701 AN: 110857 Hom.: 5804 Cov.: 22

Gnomad AFR AF: 0.621

Gnomad AMI AF: 0.308

Gnomad AMR AF: 0.267

Gnomad ASJ AF: 0.292

Gnomad EAS AF: 0.346

Gnomad SAS AF: 0.202

Gnomad FIN AF: 0.193

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.202

Gnomad OTH AF: 0.324

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

GnomAD4 genome AF: 0.331 AC: 36722 AN: 110912 Hom.: 5802 Cov.: 22 AF XY: 0.315 AC XY: 10464 AN XY: 33220

African (AFR) AF: 0.621 AC: 18830 AN: 30341

American (AMR) AF: 0.266 AC: 2786 AN: 10466

Ashkenazi Jewish (ASJ) AF: 0.292 AC: 773 AN: 2644

East Asian (EAS) AF: 0.346 AC: 1205 AN: 3480

South Asian (SAS) AF: 0.199 AC: 531 AN: 2668

European-Finnish (FIN) AF: 0.193 AC: 1144 AN: 5926

Middle Eastern (MID) AF: 0.290 AC: 62 AN: 214

European-Non Finnish (NFE) AF: 0.202 AC: 10704 AN: 52995

Other (OTH) AF: 0.319 AC: 480 AN: 1506

Alfa AF: 0.264 Hom.: 2895

Bravo AF: 0.360

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.2
DANN	Benign	0.68
PhyloP100		-0.41

Splicing

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

Other links and lift over

dbSNP: rs205828; hg19: chrX-42776949;