X-42273924-T-C

Position:

• chrX-42273924-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 0.358 in 109,791 control chromosomes in the GnomAD database, including 8,215 homozygotes. There are 10,813 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 0.36 (8215 hom., 10813 hem., cov: 21)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.468

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.784 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.42273924T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000231772	ENST00000411879.5	n.193+19116T>C		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.357 AC: 39226 AN: 109739 Hom.: 8206 Cov.: 21 AF XY: 0.336 AC XY: 10766 AN XY: 32041

Gnomad AFR AF: 0.792

Gnomad AMI AF: 0.0643

Gnomad AMR AF: 0.267

Gnomad ASJ AF: 0.179

Gnomad EAS AF: 0.165

Gnomad SAS AF: 0.184

Gnomad FIN AF: 0.172

Gnomad MID AF: 0.245

Gnomad NFE AF: 0.184

Gnomad OTH AF: 0.341

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

GnomAD4 genome AF: 0.358 AC: 39291 AN: 109791 Hom.: 8215 Cov.: 21 AF XY: 0.337 AC XY: 10813 AN XY: 32103

Gnomad4 AFR AF: 0.793

Gnomad4 AMR AF: 0.267

Gnomad4 ASJ AF: 0.179

Gnomad4 EAS AF: 0.165

Gnomad4 SAS AF: 0.184

Gnomad4 FIN AF: 0.172

Gnomad4 NFE AF: 0.184

Gnomad4 OTH AF: 0.341

Alfa AF: 0.355 Hom.: 3191

Bravo AF: 0.387

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.2
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4509495; hg19: chrX-42133177;