rs792774

Variant names:

• chr17-53025561-A-C
• rs792774

Your query was ambiguous. Multiple possible variants found:

• chr17-53025561-A-C
• chr17-53025561-A-G

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 0.399 in 151,664 control chromosomes in the GnomAD database, including 13,322 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 0.40 (13322 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.122

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.483 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: 0.399 AC: 60538 AN: 151542 Hom.: 13319 Cov.: 30

Gnomad AFR AF: 0.216

Gnomad AMI AF: 0.460

Gnomad AMR AF: 0.466

Gnomad ASJ AF: 0.441

Gnomad EAS AF: 0.226

Gnomad SAS AF: 0.375

Gnomad FIN AF: 0.532

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.487

Gnomad OTH AF: 0.407

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

GnomAD4 genome AF: 0.399 AC: 60557 AN: 151664 Hom.: 13322 Cov.: 30 AF XY: 0.401 AC XY: 29725 AN XY: 74058

Gnomad4 AFR AF: 0.216

Gnomad4 AMR AF: 0.466

Gnomad4 ASJ AF: 0.441

Gnomad4 EAS AF: 0.225

Gnomad4 SAS AF: 0.376

Gnomad4 FIN AF: 0.532

Gnomad4 NFE AF: 0.487

Gnomad4 OTH AF: 0.408

Alfa AF: 0.441 Hom.: 6445

Bravo AF: 0.386

Asia WGS AF: 0.303 AC: 1055 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.0
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs792774; hg19: chr17-51102921;