rs17778257

chr5-148825014-A-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.348 in 152,210 control chromosomes in the GnomAD database, including 9,692 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 0.35 (9692 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.67

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.22).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.384 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.348 AC: 52855 AN: 152092 Hom.: 9678 Cov.: 33

Gnomad AFR AF: 0.239

Gnomad AMI AF: 0.207

Gnomad AMR AF: 0.389

Gnomad ASJ AF: 0.413

Gnomad EAS AF: 0.394

Gnomad SAS AF: 0.397

Gnomad FIN AF: 0.474

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.376

Gnomad OTH AF: 0.362

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

GnomAD4 genome AF: 0.347 AC: 52893 AN: 152210 Hom.: 9692 Cov.: 33 AF XY: 0.354 AC XY: 26360 AN XY: 74418

Gnomad4 AFR AF: 0.239

Gnomad4 AMR AF: 0.389

Gnomad4 ASJ AF: 0.413

Gnomad4 EAS AF: 0.394

Gnomad4 SAS AF: 0.399

Gnomad4 FIN AF: 0.474

Gnomad4 NFE AF: 0.376

Gnomad4 OTH AF: 0.369

Alfa AF: 0.362 Hom.: 1454

Bravo AF: 0.335

Asia WGS AF: 0.403 AC: 1398 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.22
Cadd	Benign	17
Dann	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17778257; hg19: chr5-148204577;