chr17-10978734-G-A

Variant names:

• chr17-10978734-G-A
• rs720404

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.835 in 152,208 control chromosomes in the GnomAD database, including 53,817 homozygotes. 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 0.84 (53817 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.721
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.915 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.836 AC: 127088 AN: 152090 Hom.: 53791 Cov.: 33

Gnomad AFR AF: 0.681

Gnomad AMI AF: 0.865

Gnomad AMR AF: 0.926

Gnomad ASJ AF: 0.935

Gnomad EAS AF: 0.938

Gnomad SAS AF: 0.885

Gnomad FIN AF: 0.915

Gnomad MID AF: 0.908

Gnomad NFE AF: 0.879

Gnomad OTH AF: 0.862

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

GnomAD4 genome AF: 0.835 AC: 127156 AN: 152208 Hom.: 53817 Cov.: 33 AF XY: 0.840 AC XY: 62486 AN XY: 74412

African (AFR) AF: 0.681 AC: 28233 AN: 41474

American (AMR) AF: 0.926 AC: 14174 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.935 AC: 3247 AN: 3472

East Asian (EAS) AF: 0.937 AC: 4852 AN: 5176

South Asian (SAS) AF: 0.886 AC: 4272 AN: 4822

European-Finnish (FIN) AF: 0.915 AC: 9710 AN: 10608

Middle Eastern (MID) AF: 0.905 AC: 266 AN: 294

European-Non Finnish (NFE) AF: 0.879 AC: 59786 AN: 68026

Other (OTH) AF: 0.863 AC: 1827 AN: 2116

Alfa AF: 0.867 Hom.: 41265

Bravo AF: 0.830

Asia WGS AF: 0.908 AC: 3156 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	4.1
DANN	Benign	0.49
PhyloP100		0.72

Splicing

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

Other links and lift over

dbSNP: rs720404; hg19: chr17-10882051;