rs3027415

Positions:

• chrX-43755194-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 0.157 in 111,661 control chromosomes in the GnomAD database, including 1,371 homozygotes. There are 5,047 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 0.16 (1371 hom., 5047 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.82

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.51).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.233 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: 0.157 AC: 17557 AN: 111603 Hom.: 1373 Cov.: 23 AF XY: 0.149 AC XY: 5049 AN XY: 33797

Gnomad AFR AF: 0.0491

Gnomad AMI AF: 0.0486

Gnomad AMR AF: 0.113

Gnomad ASJ AF: 0.199

Gnomad EAS AF: 0.0210

Gnomad SAS AF: 0.0754

Gnomad FIN AF: 0.194

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.236

Gnomad OTH AF: 0.174

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

GnomAD4 genome AF: 0.157 AC: 17549 AN: 111661 Hom.: 1371 Cov.: 23 AF XY: 0.149 AC XY: 5047 AN XY: 33863

Gnomad4 AFR AF: 0.0491

Gnomad4 AMR AF: 0.112

Gnomad4 ASJ AF: 0.199

Gnomad4 EAS AF: 0.0205

Gnomad4 SAS AF: 0.0756

Gnomad4 FIN AF: 0.194

Gnomad4 NFE AF: 0.236

Gnomad4 OTH AF: 0.171

Alfa AF: 0.217 Hom.: 11895

Bravo AF: 0.149

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.51
CADD	Benign	20
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3027415; hg19: chrX-43614441;