chrX-100582827-G-A

Variant names:

• chrX-100582827-G-A
• rs7890586
• ENST00000780746.1:n.77+23367C>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+23367C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.226 in 110,481 control chromosomes in the GnomAD database, including 2,760 homozygotes. There are 7,060 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 0.23 (2760 hom., 7060 hem., cov: 22)
• Consequence: ENSG00000301679 ENST00000780746.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.700
• Publications: 3 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=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.422 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
ENSG00000301679	ENST00000780746.1	n.77+23367C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.226 AC: 24917 AN: 110427 Hom.: 2757 Cov.: 22

Gnomad AFR AF: 0.429

Gnomad AMI AF: 0.168

Gnomad AMR AF: 0.159

Gnomad ASJ AF: 0.201

Gnomad EAS AF: 0.125

Gnomad SAS AF: 0.325

Gnomad FIN AF: 0.0944

Gnomad MID AF: 0.153

Gnomad NFE AF: 0.142

Gnomad OTH AF: 0.222

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

GnomAD4 genome AF: 0.226 AC: 24932 AN: 110481 Hom.: 2760 Cov.: 22 AF XY: 0.215 AC XY: 7060 AN XY: 32819

African (AFR) AF: 0.428 AC: 12956 AN: 30266

American (AMR) AF: 0.158 AC: 1643 AN: 10369

Ashkenazi Jewish (ASJ) AF: 0.201 AC: 531 AN: 2639

East Asian (EAS) AF: 0.125 AC: 437 AN: 3496

South Asian (SAS) AF: 0.325 AC: 849 AN: 2609

European-Finnish (FIN) AF: 0.0944 AC: 558 AN: 5910

Middle Eastern (MID) AF: 0.164 AC: 35 AN: 214

European-Non Finnish (NFE) AF: 0.142 AC: 7471 AN: 52791

Other (OTH) AF: 0.224 AC: 339 AN: 1514

Alfa AF: 0.200 Hom.: 5108

Bravo AF: 0.240

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.4
DANN	Benign	0.75
PhyloP100		0.70

Splicing

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

Other links and lift over

dbSNP: rs7890586; hg19: chrX-99837824;