chrX-98411382-T-C

Position:

• chrX-98411382-T-C

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 0.311 in 109,947 control chromosomes in the GnomAD database, including 4,227 homozygotes. There are 10,140 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 0.31 (4227 hom., 10140 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.00

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.729 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.311 AC: 34214 AN: 109893 Hom.: 4237 Cov.: 22 AF XY: 0.314 AC XY: 10121 AN XY: 32249

Gnomad AFR AF: 0.218

Gnomad AMI AF: 0.176

Gnomad AMR AF: 0.479

Gnomad ASJ AF: 0.362

Gnomad EAS AF: 0.753

Gnomad SAS AF: 0.531

Gnomad FIN AF: 0.217

Gnomad MID AF: 0.347

Gnomad NFE AF: 0.301

Gnomad OTH AF: 0.351

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

GnomAD4 genome AF: 0.311 AC: 34215 AN: 109947 Hom.: 4227 Cov.: 22 AF XY: 0.314 AC XY: 10140 AN XY: 32313

Gnomad4 AFR AF: 0.218

Gnomad4 AMR AF: 0.479

Gnomad4 ASJ AF: 0.362

Gnomad4 EAS AF: 0.753

Gnomad4 SAS AF: 0.530

Gnomad4 FIN AF: 0.217

Gnomad4 NFE AF: 0.301

Gnomad4 OTH AF: 0.352

Alfa AF: 0.335 Hom.: 5588

Bravo AF: 0.332

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.024
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2105183; hg19: chrX-97666380;