rs3027898

chrX-154010439-C-AchrX-154010439-C-G

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 0.655 in 6,095 control chromosomes in the GnomAD database, including 1,151 homozygotes. There are 915 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 0.68 (19380 hom., 21574 hem., cov: 22)
  • Exomes 𝑓: 0.66 (1151 hom. 915 hem.)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.392

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAdExome4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.793 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: 0.683 AC: 75018 AN: 109876 Hom.: 19389 Cov.: 22 AF XY: 0.670 AC XY: 21549 AN XY: 32180

Gnomad AFR AF: 0.570

Gnomad AMI AF: 0.960

Gnomad AMR AF: 0.543

Gnomad ASJ AF: 0.739

Gnomad EAS AF: 0.212

Gnomad SAS AF: 0.358

Gnomad FIN AF: 0.793

Gnomad MID AF: 0.650

Gnomad NFE AF: 0.805

Gnomad OTH AF: 0.647

GnomAD4 exome AF: 0.655 AC: 3994 AN: 6095 Hom.: 1151 AF XY: 0.673 AC XY: 915 AN XY: 1359

Gnomad4 AFR exome AF: 0.496

Gnomad4 AMR exome AF: 0.483

Gnomad4 ASJ exome AF: 0.750

Gnomad4 EAS exome AF: 0.209

Gnomad4 SAS exome AF: 0.364

Gnomad4 FIN exome AF: 0.819

Gnomad4 NFE exome AF: 0.820

Gnomad4 OTH exome AF: 0.708

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.682 AC: 75019 AN: 109924 Hom.: 19380 Cov.: 22 AF XY: 0.669 AC XY: 21574 AN XY: 32238

Gnomad4 AFR AF: 0.570

Gnomad4 AMR AF: 0.542

Gnomad4 ASJ AF: 0.739

Gnomad4 EAS AF: 0.212

Gnomad4 SAS AF: 0.360

Gnomad4 FIN AF: 0.793

Gnomad4 NFE AF: 0.805

Gnomad4 OTH AF: 0.637

Alfa AF: 0.752 Hom.: 31021

Bravo AF: 0.658

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
Cadd	Benign	0.88
Dann	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3027898; hg19: chrX-153275890; COSMIC: COSV64110208;