rs7878264

Variant names:

• chrX-71207339-A-G
• rs7878264

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

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 0.60 (14906 hom., 15042 hem., cov: 18)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.23
• Publications: 1 publications found

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).

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: 0.596 AC: 61028 AN: 102472 Hom.: 14897 Cov.: 18

Gnomad AFR AF: 0.824

Gnomad AMI AF: 0.669

Gnomad AMR AF: 0.629

Gnomad ASJ AF: 0.677

Gnomad EAS AF: 0.752

Gnomad SAS AF: 0.607

Gnomad FIN AF: 0.393

Gnomad MID AF: 0.668

Gnomad NFE AF: 0.464

Gnomad OTH AF: 0.631

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

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.596 AC: 61071 AN: 102499 Hom.: 14906 Cov.: 18 AF XY: 0.587 AC XY: 15042 AN XY: 25627

African (AFR) AF: 0.824 AC: 23298 AN: 28271

American (AMR) AF: 0.629 AC: 5938 AN: 9437

Ashkenazi Jewish (ASJ) AF: 0.677 AC: 1729 AN: 2554

East Asian (EAS) AF: 0.752 AC: 2241 AN: 2982

South Asian (SAS) AF: 0.607 AC: 1183 AN: 1950

European-Finnish (FIN) AF: 0.393 AC: 1817 AN: 4625

Middle Eastern (MID) AF: 0.680 AC: 136 AN: 200

European-Non Finnish (NFE) AF: 0.464 AC: 23408 AN: 50437

Other (OTH) AF: 0.637 AC: 901 AN: 1415

Alfa AF: 0.543 Hom.: 4090

Bravo AF: 0.625

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.7
DANN	Benign	0.40
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs7878264; hg19: chrX-70427189;