17-45317812-A-G

Variant names:

• chr17-45317812-A-G
• rs4792849

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.774 in 151,028 control chromosomes in the GnomAD database, including 46,332 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 0.77 (46332 hom., cov: 25)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.782
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.45).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.942 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: 0.774 AC: 116835 AN: 150912 Hom.: 46270 Cov.: 25

Gnomad AFR AF: 0.950

Gnomad AMI AF: 0.596

Gnomad AMR AF: 0.635

Gnomad ASJ AF: 0.662

Gnomad EAS AF: 0.501

Gnomad SAS AF: 0.722

Gnomad FIN AF: 0.759

Gnomad MID AF: 0.712

Gnomad NFE AF: 0.735

Gnomad OTH AF: 0.745

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

GnomAD4 genome AF: 0.774 AC: 116955 AN: 151028 Hom.: 46332 Cov.: 25 AF XY: 0.771 AC XY: 56842 AN XY: 73708

African (AFR) AF: 0.950 AC: 39127 AN: 41186

American (AMR) AF: 0.635 AC: 9593 AN: 15108

Ashkenazi Jewish (ASJ) AF: 0.662 AC: 2292 AN: 3464

East Asian (EAS) AF: 0.501 AC: 2532 AN: 5056

South Asian (SAS) AF: 0.721 AC: 3439 AN: 4768

European-Finnish (FIN) AF: 0.759 AC: 7871 AN: 10372

Middle Eastern (MID) AF: 0.707 AC: 208 AN: 294

European-Non Finnish (NFE) AF: 0.735 AC: 49805 AN: 67796

Other (OTH) AF: 0.745 AC: 1549 AN: 2080

Alfa AF: 0.770 Hom.: 27017

Bravo AF: 0.772

Asia WGS AF: 0.630 AC: 2194 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.45
CADD	Benign	0.73
DANN	Benign	0.42
PhyloP100		-0.78

Splicing

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

Other links and lift over

dbSNP: rs4792849; hg19: chr17-43395178;