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).

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: 0.496 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 v4.3

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

Other links and lift over

dbSNP: rs1977719; hg19: chrX-78397143;