rs17826780

Variant names:

• chr4-54589777-C-T
• rs17826780

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 0.108 in 152,116 control chromosomes in the GnomAD database, including 944 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 0.11 (944 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.867

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.113 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: 0.108 AC: 16480 AN: 151998 Hom.: 943 Cov.: 32

Gnomad AFR AF: 0.116

Gnomad AMI AF: 0.140

Gnomad AMR AF: 0.0703

Gnomad ASJ AF: 0.0775

Gnomad EAS AF: 0.0275

Gnomad SAS AF: 0.116

Gnomad FIN AF: 0.146

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.114

Gnomad OTH AF: 0.102

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

GnomAD4 genome AF: 0.108 AC: 16503 AN: 152116 Hom.: 944 Cov.: 32 AF XY: 0.109 AC XY: 8088 AN XY: 74380

Gnomad4 AFR AF: 0.116

Gnomad4 AMR AF: 0.0702

Gnomad4 ASJ AF: 0.0775

Gnomad4 EAS AF: 0.0272

Gnomad4 SAS AF: 0.116

Gnomad4 FIN AF: 0.146

Gnomad4 NFE AF: 0.114

Gnomad4 OTH AF: 0.106

Alfa AF: 0.111 Hom.: 428

Bravo AF: 0.102

Asia WGS AF: 0.0910 AC: 316 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.66
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17826780; hg19: chr4-55455944;