X-30823771-C-T

Variant names:

• chrX-30823771-C-T
• rs966446

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 0.502 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
• Publications: 5 publications found

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 (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

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

African (AFR) AF: 0.252 AC: 7662 AN: 30368

American (AMR) AF: 0.466 AC: 4808 AN: 10309

Ashkenazi Jewish (ASJ) AF: 0.631 AC: 1661 AN: 2632

East Asian (EAS) AF: 0.520 AC: 1803 AN: 3467

South Asian (SAS) AF: 0.572 AC: 1490 AN: 2605

European-Finnish (FIN) AF: 0.694 AC: 3944 AN: 5679

Middle Eastern (MID) AF: 0.607 AC: 130 AN: 214

European-Non Finnish (NFE) AF: 0.620 AC: 32602 AN: 52583

Other (OTH) AF: 0.517 AC: 777 AN: 1504

Alfa AF: 0.518 Hom.: 21242

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
PhyloP100		-0.097

Splicing

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

Other links and lift over

dbSNP: rs966446; hg19: chrX-30841888;