rs720404

Variant names:

• chr17-10978734-G-A
• rs720404

Your query was ambiguous. Multiple possible variants found:

• chr17-10978734-G-A
• chr17-10978734-G-C
• chr17-10978734-G-T

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 0.835 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.836 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

Gnomad4 AFR AF: 0.681

Gnomad4 AMR AF: 0.926

Gnomad4 ASJ AF: 0.935

Gnomad4 EAS AF: 0.937

Gnomad4 SAS AF: 0.886

Gnomad4 FIN AF: 0.915

Gnomad4 NFE AF: 0.879

Gnomad4 OTH AF: 0.863

Alfa AF: 0.869 Hom.: 28665

Bravo AF: 0.830

Asia WGS AF: 0.908 AC: 3156 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs720404; hg19: chr17-10882051;