rs7066438

Variant names:

• chrX-71179969-A-T
• rs7066438

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;