chrX-30823771-C-T

Variant names:

• chrX-30823771-C-T
• rs966446

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.502 in 110,029 control chromosomes in the GnomAD database, including 10,684 homozygotes. There are 16,423 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 0.50 (10684 hom., 16423 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0970

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.614 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: 0.502 AC: 55257 AN: 109974 Hom.: 10691 Cov.: 22 AF XY: 0.508 AC XY: 16409 AN XY: 32306

Gnomad AFR AF: 0.252

Gnomad AMI AF: 0.567

Gnomad AMR AF: 0.466

Gnomad ASJ AF: 0.631

Gnomad EAS AF: 0.520

Gnomad SAS AF: 0.573

Gnomad FIN AF: 0.694

Gnomad MID AF: 0.609

Gnomad NFE AF: 0.620

Gnomad OTH AF: 0.522

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

GnomAD4 genome AF: 0.502 AC: 55256 AN: 110029 Hom.: 10684 Cov.: 22 AF XY: 0.507 AC XY: 16423 AN XY: 32371

Gnomad4 AFR AF: 0.252

Gnomad4 AMR AF: 0.466

Gnomad4 ASJ AF: 0.631

Gnomad4 EAS AF: 0.520

Gnomad4 SAS AF: 0.572

Gnomad4 FIN AF: 0.694

Gnomad4 NFE AF: 0.620

Gnomad4 OTH AF: 0.517

Alfa AF: 0.576 Hom.: 13850

Bravo AF: 0.474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	3.6
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs966446; hg19: chrX-30841888;