rs1977719

Variant names:

• chrX-79141646-C-T
• rs1977719

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 0.50 (10067 hom., 9398 hem., cov: 16)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.999
• 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=-0.92).

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.496 AC: 47281 AN: 95328 Hom.: 10073 Cov.: 16

Gnomad AFR AF: 0.413

Gnomad AMI AF: 0.568

Gnomad AMR AF: 0.396

Gnomad ASJ AF: 0.488

Gnomad EAS AF: 0.393

Gnomad SAS AF: 0.515

Gnomad FIN AF: 0.402

Gnomad MID AF: 0.492

Gnomad NFE AF: 0.571

Gnomad OTH AF: 0.492

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: 0.496 AC: 47273 AN: 95332 Hom.: 10067 Cov.: 16 AF XY: 0.434 AC XY: 9398 AN XY: 21630

African (AFR) AF: 0.413 AC: 10805 AN: 26176

American (AMR) AF: 0.396 AC: 3470 AN: 8772

Ashkenazi Jewish (ASJ) AF: 0.488 AC: 1192 AN: 2443

East Asian (EAS) AF: 0.393 AC: 1218 AN: 3098

South Asian (SAS) AF: 0.514 AC: 1025 AN: 1996

European-Finnish (FIN) AF: 0.402 AC: 1183 AN: 2942

Middle Eastern (MID) AF: 0.488 AC: 83 AN: 170

European-Non Finnish (NFE) AF: 0.571 AC: 27310 AN: 47825

Other (OTH) AF: 0.492 AC: 635 AN: 1290

Alfa AF: 0.545 Hom.: 3512

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.12
DANN	Benign	0.22
PhyloP100		-1.0

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1977719;

hg19: chrX-78397143;