X-26351782-A-C

Variant names:

• chrX-26351782-A-C
• rs6526555
• ENST00000779285.1:n.930-970T>G

Variant summary

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

The ENST00000779285.1(ENSG00000301494):​n.930-970T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.406 in 110,829 control chromosomes in the GnomAD database, including 8,109 homozygotes. There are 13,218 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 0.41 (8109 hom., 13218 hem., cov: 23)
• Consequence: ENSG00000301494 ENST00000779285.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.661
• Publications: 1 publications found

Genes affected

ENSG00000301494 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.679 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
ENSG00000301494	ENST00000779285.1	n.930-970T>G		intron_variant	Intron 9 of 9

Frequencies

GnomAD3 genomes AF: 0.406 AC: 44953 AN: 110774 Hom.: 8099 Cov.: 23

Gnomad AFR AF: 0.687

Gnomad AMI AF: 0.390

Gnomad AMR AF: 0.489

Gnomad ASJ AF: 0.305

Gnomad EAS AF: 0.534

Gnomad SAS AF: 0.465

Gnomad FIN AF: 0.276

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.238

Gnomad OTH AF: 0.399

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

GnomAD4 genome AF: 0.406 AC: 45017 AN: 110829 Hom.: 8109 Cov.: 23 AF XY: 0.399 AC XY: 13218 AN XY: 33099

African (AFR) AF: 0.687 AC: 20864 AN: 30371

American (AMR) AF: 0.490 AC: 5116 AN: 10443

Ashkenazi Jewish (ASJ) AF: 0.305 AC: 802 AN: 2629

East Asian (EAS) AF: 0.533 AC: 1856 AN: 3482

South Asian (SAS) AF: 0.464 AC: 1221 AN: 2631

European-Finnish (FIN) AF: 0.276 AC: 1631 AN: 5909

Middle Eastern (MID) AF: 0.265 AC: 57 AN: 215

European-Non Finnish (NFE) AF: 0.238 AC: 12604 AN: 52974

Other (OTH) AF: 0.402 AC: 603 AN: 1501

Alfa AF: 0.336 Hom.: 20820

Bravo AF: 0.443

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.3
DANN	Benign	0.60
PhyloP100		-0.66

Splicing

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

Other links and lift over

dbSNP: rs6526555; hg19: chrX-26369899;