rs4792855

Variant names:

• chr17-45382331-C-T
• rs4792855

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 0.466 in 152,090 control chromosomes in the GnomAD database, including 16,623 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 0.47 (16623 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.268
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.482 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: 0.466 AC: 70874 AN: 151968 Hom.: 16598 Cov.: 33

Gnomad AFR AF: 0.488

Gnomad AMI AF: 0.485

Gnomad AMR AF: 0.447

Gnomad ASJ AF: 0.465

Gnomad EAS AF: 0.372

Gnomad SAS AF: 0.467

Gnomad FIN AF: 0.468

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.464

Gnomad OTH AF: 0.472

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

GnomAD4 genome AF: 0.466 AC: 70934 AN: 152090 Hom.: 16623 Cov.: 33 AF XY: 0.464 AC XY: 34464 AN XY: 74312

African (AFR) AF: 0.488 AC: 20237 AN: 41486

American (AMR) AF: 0.448 AC: 6841 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.465 AC: 1614 AN: 3472

East Asian (EAS) AF: 0.372 AC: 1927 AN: 5174

South Asian (SAS) AF: 0.466 AC: 2249 AN: 4822

European-Finnish (FIN) AF: 0.468 AC: 4932 AN: 10544

Middle Eastern (MID) AF: 0.412 AC: 121 AN: 294

European-Non Finnish (NFE) AF: 0.464 AC: 31574 AN: 67992

Other (OTH) AF: 0.473 AC: 998 AN: 2112

Alfa AF: 0.465 Hom.: 24597

Bravo AF: 0.469

Asia WGS AF: 0.456 AC: 1584 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.2
DANN	Benign	0.59
PhyloP100		-0.27

Splicing

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

Other links and lift over

dbSNP: rs4792855; hg19: chr17-43459697;