rs1415270

chrX-67744643-G-AchrX-67744643-G-CchrX-67744643-G-T

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 0.619 in 110,865 control chromosomes in the GnomAD database, including 18,291 homozygotes. There are 21,023 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 0.62 (18291 hom., 21023 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.275

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.97 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: 0.620 AC: 68668 AN: 110810 Hom.: 18299 Cov.: 23 AF XY: 0.636 AC XY: 21006 AN XY: 33036

Gnomad AFR AF: 0.130

Gnomad AMI AF: 0.875

Gnomad AMR AF: 0.788

Gnomad ASJ AF: 0.796

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.901

Gnomad FIN AF: 0.821

Gnomad MID AF: 0.658

Gnomad NFE AF: 0.795

Gnomad OTH AF: 0.653

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

GnomAD4 genome AF: 0.619 AC: 68662 AN: 110865 Hom.: 18291 Cov.: 23 AF XY: 0.635 AC XY: 21023 AN XY: 33101

Gnomad4 AFR AF: 0.130

Gnomad4 AMR AF: 0.789

Gnomad4 ASJ AF: 0.796

Gnomad4 EAS AF: 0.998

Gnomad4 SAS AF: 0.902

Gnomad4 FIN AF: 0.821

Gnomad4 NFE AF: 0.795

Gnomad4 OTH AF: 0.658

Alfa AF: 0.741 Hom.: 10959

Bravo AF: 0.603

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	1.4
Dann	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1415270; hg19: chrX-66964485;