rs1415270

Variant names:

• chrX-67744643-G-A
• rs1415270

Your query was ambiguous. Multiple possible variants found:

• chrX-67744643-G-A
• chrX-67744643-G-C
• chrX-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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;