rs3027415

Variant names:

• chrX-43755194-T-C
• rs3027415

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;