X-100584573-C-A

Variant names:

• chrX-100584573-C-A
• rs11798018
• ENST00000780746.1:n.77+21621G>T

Variant summary

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

The ENST00000780746.1(ENSG00000301679):​n.77+21621G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.254 in 111,273 control chromosomes in the GnomAD database, including 3,389 homozygotes. There are 8,766 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 0.25 (3389 hom., 8766 hem., cov: 23)
• Consequence: ENSG00000301679 ENST00000780746.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.86
• Publications: 8 publications found

Genes affected

ENSG00000301679 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.692 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000780746.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000301679	ENST00000780746.1		n.77+21621G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.255 AC: 28314 AN: 111218 Hom.: 3393 Cov.: 23

Gnomad AFR AF: 0.0509

Gnomad AMI AF: 0.379

Gnomad AMR AF: 0.358

Gnomad ASJ AF: 0.241

Gnomad EAS AF: 0.715

Gnomad SAS AF: 0.393

Gnomad FIN AF: 0.384

Gnomad MID AF: 0.248

Gnomad NFE AF: 0.299

Gnomad OTH AF: 0.272

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

GnomAD4 genome AF: 0.254 AC: 28304 AN: 111273 Hom.: 3389 Cov.: 23 AF XY: 0.262 AC XY: 8766 AN XY: 33511

African (AFR) AF: 0.0508 AC: 1567 AN: 30842

American (AMR) AF: 0.358 AC: 3755 AN: 10484

Ashkenazi Jewish (ASJ) AF: 0.241 AC: 634 AN: 2636

East Asian (EAS) AF: 0.715 AC: 2501 AN: 3498

South Asian (SAS) AF: 0.392 AC: 1033 AN: 2633

European-Finnish (FIN) AF: 0.384 AC: 2270 AN: 5915

Middle Eastern (MID) AF: 0.240 AC: 52 AN: 217

European-Non Finnish (NFE) AF: 0.299 AC: 15830 AN: 52861

Other (OTH) AF: 0.269 AC: 407 AN: 1515

Alfa AF: 0.283 Hom.: 18229

Bravo AF: 0.251

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	1.4
DANN	Benign	0.68
PhyloP100		-1.9
PromoterAI		-0.039	Neutral

Splicing

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

Other links and lift over

dbSNP: rs11798018; hg19: chrX-99839570;