rs7881412

chrX-6251419-G-A

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 0.112 in 111,342 control chromosomes in the GnomAD database, including 694 homozygotes. There are 3,502 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 0.11 (694 hom., 3502 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.447

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.204 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: 0.112 AC: 12478 AN: 111291 Hom.: 694 Cov.: 23 AF XY: 0.104 AC XY: 3499 AN XY: 33525

Gnomad AFR AF: 0.209

Gnomad AMI AF: 0.253

Gnomad AMR AF: 0.0591

Gnomad ASJ AF: 0.107

Gnomad EAS AF: 0.00196

Gnomad SAS AF: 0.0873

Gnomad FIN AF: 0.0693

Gnomad MID AF: 0.0890

Gnomad NFE AF: 0.0797

Gnomad OTH AF: 0.0933

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

GnomAD4 genome AF: 0.112 AC: 12480 AN: 111342 Hom.: 694 Cov.: 23 AF XY: 0.104 AC XY: 3502 AN XY: 33586

Gnomad4 AFR AF: 0.208

Gnomad4 AMR AF: 0.0590

Gnomad4 ASJ AF: 0.107

Gnomad4 EAS AF: 0.00168

Gnomad4 SAS AF: 0.0873

Gnomad4 FIN AF: 0.0693

Gnomad4 NFE AF: 0.0797

Gnomad4 OTH AF: 0.0922

Alfa AF: 0.0844 Hom.: 1474

Bravo AF: 0.116

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	0.54
Dann	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7881412; hg19: chrX-6169460;