X-78916693-C-T

Variant names:

• chrX-78916693-C-T
• rs10521387

Variant summary

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

The variant allele was found at a frequency of 0.0592 in 111,361 control chromosomes in the GnomAD database, including 597 homozygotes. There are 2,253 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 0.059 (597 hom., 2253 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.820
• Publications: 0 publications found

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 (EAS) allele frequency at 95% confidence interval = 0.469 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

Frequencies

GnomAD3 genomes AF: 0.0592 AC: 6589 AN: 111306 Hom.: 595 Cov.: 23

Gnomad AFR AF: 0.0114

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.228

Gnomad ASJ AF: 0.0390

Gnomad EAS AF: 0.488

Gnomad SAS AF: 0.266

Gnomad FIN AF: 0.0181

Gnomad MID AF: 0.00847

Gnomad NFE AF: 0.0210

Gnomad OTH AF: 0.0726

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

GnomAD4 genome AF: 0.0592 AC: 6596 AN: 111361 Hom.: 597 Cov.: 23 AF XY: 0.0670 AC XY: 2253 AN XY: 33609

African (AFR) AF: 0.0114 AC: 350 AN: 30790

American (AMR) AF: 0.229 AC: 2387 AN: 10431

Ashkenazi Jewish (ASJ) AF: 0.0390 AC: 103 AN: 2643

East Asian (EAS) AF: 0.488 AC: 1718 AN: 3519

South Asian (SAS) AF: 0.266 AC: 703 AN: 2639

European-Finnish (FIN) AF: 0.0181 AC: 109 AN: 6013

Middle Eastern (MID) AF: 0.00926 AC: 2 AN: 216

European-Non Finnish (NFE) AF: 0.0210 AC: 1113 AN: 52923

Other (OTH) AF: 0.0736 AC: 111 AN: 1508

Alfa AF: 0.0430 Hom.: 244

Bravo AF: 0.0786

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.64
DANN	Benign	0.38
PhyloP100		-0.82

Splicing

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

Other links and lift over

dbSNP: rs10521387; hg19: chrX-78172190;