rs7066438

chrX-71179969-A-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 0.407 in 109,985 control chromosomes in the GnomAD database, including 7,954 homozygotes. There are 12,385 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 0.41 (7954 hom., 12385 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.29

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.673 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: 0.407 AC: 44734 AN: 109931 Hom.: 7951 Cov.: 22 AF XY: 0.382 AC XY: 12345 AN XY: 32275

Gnomad AFR AF: 0.681

Gnomad AMI AF: 0.402

Gnomad AMR AF: 0.304

Gnomad ASJ AF: 0.506

Gnomad EAS AF: 0.198

Gnomad SAS AF: 0.219

Gnomad FIN AF: 0.225

Gnomad MID AF: 0.550

Gnomad NFE AF: 0.309

Gnomad OTH AF: 0.426

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

GnomAD4 genome AF: 0.407 AC: 44780 AN: 109985 Hom.: 7954 Cov.: 22 AF XY: 0.383 AC XY: 12385 AN XY: 32339

Gnomad4 AFR AF: 0.681

Gnomad4 AMR AF: 0.303

Gnomad4 ASJ AF: 0.506

Gnomad4 EAS AF: 0.197

Gnomad4 SAS AF: 0.220

Gnomad4 FIN AF: 0.225

Gnomad4 NFE AF: 0.309

Gnomad4 OTH AF: 0.429

Alfa AF: 0.368 Hom.: 2519

Bravo AF: 0.428

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	3.7
Dann	Benign	0.88

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7066438; hg19: chrX-70399819;